bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning
Authors: Quince Christopher , Connelly Stephanie , Raguideau Sébastien , Alneberg Johannes , Shin Seung Gu , Collins Gavin , Eren A. Murat 
Published: September 2016

AbstractBackgroundWe introduceDESMANfor De novo Extraction of Strains from MetAgeNomes. Metagenome sequencing generates short reads from throughout the genomes of a microbial community. Increasingly large, multi-sample metagenomes, stratified in space and time are being generated from communities with thousands of species. Repeats result in fragmentary co-assemblies with potentially millions of contigs. Contigs can be binned into metagenome assembled genomes (MAGs) but strain level variation will remain. DESMAN identifies variants on core genes, then uses co-occurrence across samples to link variants into strain sequences and abundance profiles. These strain profiles are then searched for on non-core genes to determine the accessory genes present in each strain.ResultsWe validatedDESMANon a synthetic twenty genome community with 64 samples. We could resolve the fiveE. colistrains present with 99.58% accuracy across core gene variable sites and their gene complement with 95.7% accuracy. Similarly, on real fecal metagenomes from the 2011E. coli(STEC) O104:H4 outbreak, the outbreak strain was reconstructed with 99.8% core sequence accuracy. Application to an anaerobic digester metagenome time series reveals that strain level variation is endemic with 16 out of 26 MAGs (61.5%) examined exhibiting two strains. In almost all cases the strain proportions were not statistically different between replicate reactors, suggesting intra-species niche partitioning. The only exception being when the two strains had almost identical gene complement and, hence, functional capability.ConclusionsDESMANwill provide a provide a powerful tool forde novoresolution of fine-scale variation in microbial communities. It is available as open source software fromhttps://github.com/chrisquince/DESMAN.
Specification and empirical exploration of a usability concept in the workplace
Authors: Windlinger Lukas , Nenonen Suvi , Airo Kaisa 
Published: September 2016

PurposeBuilding on fundamental work on usability of workplaces, this paper aims to extend the perspective of usability as an approach in delivering workplace solutions. To explore the content and implications of usability, the concept is differentiated into two sub-concepts: usefulness and user-friendliness.Design/methodology/approachThe theoretical rationale for the proposed conceptual specification is presented and explored using data from two independent research projects: a qualitative interview study in an office relocation project in Finland and a quantitative survey study of 1,420 office users of 43 buildings in Switzerland. The goal of the empirical research is to capture the elements of user experience connected to usability using the distinction between usefulness and user-friendliness.FindingsThe results from both studies show that perceived support of work activities by workspaces in relation to work tasks is the main element of usefulness. User-friendliness incorporates comfort and control as the two most important aspects. Correlations between usefulness and user-friendliness and outcomes of usable workspace design are low for self-assessed performance, moderate for job satisfaction and high for work area satisfaction.Practical implicationsProviding useful workplaces supports users’ job performance while designing for user-friendliness is correlated with user satisfaction.Originality/valueThe differentiation of usefulness and user-friendliness of office environments provides a new way to describe user experience. The integration of qualitative and quantitative research strategies strengthens the research evidence.
Long-run relationship between investment and maintenance in local governments
Authors: Hopland Arnt O. 
Published: September 2016

Purpose
The purpose of the paper is to analyze the relationship between maintenance of existent and investment in new infrastructure in Norwegian local governments.

Design/methodology/approach
A reduced form vector autoregressive system is estimated using a 29-year-long panel data set for the Norwegian local governments.

Findings
The data reveal that increased investment in new infrastructure sparks little, if any, increase in maintenance. The results also indicate that increased maintenance expenditures spark new investments. Because more investments mean more infrastructure and adequate maintenance should give that investments are not caused by maintenance, the results suggest that the local governments have not optimized their maintenance scheduling in this period.

Originality/value
Even though maintenance and investment are large expenditures that both serve as inputs to the stock of infrastructure, little is known about the relationship between the two. The findings in this paper suggests that Norwegian local governments have not planned their maintenance and investments well in the past, and this can be part of the explanation as to why local public infrastructure in Norway is presently in poor condition.
Green building for office interiors: challenges and opportunities
Authors: Gou Zhonghua 
Published: September 2016

PurposeThis paper aims to examine the concept and practice of green building for office interiors: whether the green intent can be effectively implemented in an interior retrofitting project.Design/methodology/approachReviewing green building rating systems for interiors, examining certified interior projects and interviewing occupants working in certified green offices.FindingsThe green building credits for interiors fall into three relational layers: the urban context, the host building and interior fit-outs. Most projects under study performed well on credits for interior fit-outs (e.g. low emitting materials, energy efficient equipment and appliances, etc.), while underperformed on credits for its host building (e.g. air-conditioning systems, ventilation, etc.). The latter might more significantly affect working experience. The other important green aspects, such as daylight availability, facilities accessibility, might be subject to its location and urban context.Research limitations/implicationsThis article presents a multi-examination of green interiors. The data came from second-hand Leadership in Energy and Environmental Design scorecards and qualitative interviews. More quantitative surveys are expected to be conducted.Practical implicationsGreen interior retrofitting should go beyond selecting environmental-friendly finishes and furniture or resource-efficient fixtures and appliances. It should proactively start from assessing the environmental performance of the host building and its urban context.Originality/valueMost research looked at green building as a whole. Green interiors are actually more practical for tenants who intend to reduce their corporate environmental impacts, whereas they do not have control over whole building design and operations. This article highlights the importance of green interior retrofitting and provides guidance.
Integrating sustainability across the university curriculum
Authors: Dmochowski Jane Ellen , Garofalo Dan , Fisher Sarah , Greene Ann , Gambogi Danielle 
Published: September 2016

Purpose
Colleges and universities increasingly have the mandate and motivation to integrate sustainability into their curricula. The purpose of this paper is to share the strategy used at the University of Pennsylvania (Penn) and provide an evaluation of its success and guidance to others creating similar programs.

Design/methodology/approach
This article summarizes Penn’s Integrating Sustainability Across the Curriculum (ISAC) program. ISAC pairs Penn undergraduate research assistants with instructors in a collaborative effort to incorporate sustainability into courses.

Findings
In concert with other Penn initiatives (a course inventory, faculty discussion groups and a research network), ISAC increases Penn’s sustainability-related courses and creates dialogue regarding how various disciplines contribute to sustainability.

Practical implications
The program described in this article is replicable at other institutions. The authors demonstrate that the logistics of recruiting students and establishing the program are straightforward. Undergraduate students are on campus; their pay requirements are modest; and they are desirous of such research experiences.

Social implications
The ISAC program inculcates a cultural and behavioral shift as students and faculty approach sustainability issues collaboratively, and it facilitates the development of a shared language of environmental sustainability. Such social implications are difficult to quantify, but are nonetheless valuable outcomes.

Originality/value
The faculty–student partnership used to facilitate the integration of sustainability into courses at Penn is original. The ISAC program provides a framework for engaging students and faculty in curriculum development around sustainability in a manner that benefits the student research assistants, the participating faculty and future students.
Understanding and alleviating loneliness in later life: perspectives of older people
Authors: Sullivan Mary Pat , Victor Christina Rita , Thomas Michael 
Published: September 2016

Purpose
There is extensive empirical literature that has sought to establish the prevalence of, and risk factors for, loneliness and social isolation in later life. Traditional empirical gerontological approaches have characterised loneliness as a linear experience that is both pathological and easily relieved with external intervention. The purpose of this paper is to explore the potential of qualitative interview data to reveal the possible complexities in understanding loneliness, including conceptual considerations for the dynamic and multi-dimensional aspects of loneliness.

Design/methodology/approach
The authors draw on two different studies where the purpose was to qualitatively examine the meaning of loneliness in the lives of older people and how they understood loneliness in the context of their daily life (n=37).

Findings
Interviews with “lonely” older people revealed that loneliness is a complex and dynamic experience. The authors also identified a range of internal and external factors that contribute to vulnerability for loneliness as well as resources to alleviate it.

Originality/value
The dynamic and multi-dimensional characteristics of loneliness in older people may help explain why community-based interventions to diminish it may be so challenging.
Mixed or merged? Integration as the real challenge for mixed methods
Authors: Bazeley Pat 
Published: September 2016

Purpose
Giampietro Gobo called for new methods that combine qualitative and quantitative approaches in a single instrument, suggesting this was the next challenge facing social research and mixed methods in particular. The purpose of this paper is to respond to that challenge.

Design/methodology/approach
An overview of methods, demonstrating their inherently mixed qualities, with special emphasis on a range of methods that can be classified as merged.

Findings
The real challenge is not to find merged methods, but to ensure integration of the quantitative and qualitative aspects of the methods used during the analysis and writing processes.

Practical implications
Researchers need to be alerted to the mixed elements within their work, to learn how to better tap into these and to exploit the integrative potential of their methods during analysis and writing. Researchers need more “rounded” methods training.

Originality/value
This paper refocuses the challenge facing mixed methods research.
Why “merged” methods realize a higher integration than “mixed” methods: a reply
Authors: Gobo Giampietro 
Published: September 2016

Purpose
After the initial life (which coincides with the origins of social research in the 1850s, and lasts until 1940s), mixed methods revive at the beginning of 1970s. However, this second life (or renaissance) receives the deleterious imprinting of quantitative methods. In fact, some of the old positivist assumptions are still reproduced and active in most of mixed methods research. This imprinting is traceable in the ambiguity (and purposive semantic stretching) of the term “qualitative”: from the 1990s, it encompasses almost everything (even approaches considered positivistic in the 1950s!). Whereby the semantical extension of the term “qualitative” has become a sort of Trojan horse for a new legitimation of many quantitative and positivist researchers: a great swindle. Today “qualitative” is nonsense and acts as a bug, which muddies the qualitative-quantitative debate. For this reason, it would be better to remove the bug (i.e. to discharge the term “qualitative” from the language of social research and methodology), reset and start over from the level of specific research methods, considering carefully and balancing their diversity before mixing them. The purpose of this paper is to outline two (complementary) ways of integration of methods (“mixed” and “merged”), arguing that “merged” methods realize a higher integration than “mixed” methods, because the former overcome some weaknesses of the latter.

Design/methodology/approach
A semantic and pragmatic analysis of the term “qualitative.”

Findings
In social and behavioral sciences, the second life of mixed methods has been heavily affected by old positivist and quantitative assumptions.

Research limitations/implications
The term “qualitative” should be discharged from the language of social research and methodology.

Practical implications
The coveted integration in “mixed” methods, could be better pursed through “merged” methods.

Social implications
Disentangling the strands of a debate (the qualitative-quantitative one) become muddy.

Originality/value
An alternative framework, to interpret the mixed methods history and their recent developments, has been proposed.
How did the domestication of Fertile Crescent grain crops increase their yields?
Authors: Preece Catherine , Livarda Alexandra , Christin Pascal‐Antoine , Wallace Michael , Martin Gemma , Charles Michael , Jones Glynis , Rees Mark , Osborne Colin P. 
Published: September 2016

Summary

The origins of agriculture, 10 000 years ago, led to profound changes in the biology of plants exploited as grain crops, through the process of domestication. This special case of evolution under cultivation led to domesticated cereals and pulses requiring humans for their dispersal, but the accompanying mechanisms causing higher productivity in these plants remain unknown. The classical view of crop domestication is narrow, focusing on reproductive and seed traits including the dispersal, dormancy and size of seeds, without considering whole‐plant characteristics. However, the effects of initial domestication events can be inferred from consistent differences between traditional landraces and their wild progenitors.

We studied how domestication increased the yields of Fertile Crescent cereals and pulses using a greenhouse experiment to compare landraces with wild progenitors. We grew eight crops: barley, einkorn and emmer wheat, oat, rye, chickpea, lentil and pea. In each case, comparison of multiple landraces with their wild progenitors enabled us to quantify the effects of domestication rather than subsequent crop diversification. To reveal the mechanisms underpinning domestication‐linked yield increases, we measured traits beyond those classically associated with domestication, including the rate and duration of growth, reproductive allocation, plant size and also seed mass and number.

Cereal and pulse crops had on average 50% higher yields than their wild progenitors, resulting from a 40% greater final plant size, 90% greater individual seed mass and 38% less chaff or pod material, although this varied between species. Cereal crops also had a higher seed number per spike compared with their wild ancestors. However, there were no differences in growth rate, total seed number, proportion of reproductive biomass or the duration of growth.

The domestication of Fertile Crescent crops resulted in larger seed size leading to a larger plant size, and also a reduction in chaff, with no decrease in seed number per individual, which proved a powerful package of traits for increasing yield. We propose that the important steps in the domestication process should be reconsidered, and the domestication syndrome broadened to include a wider range of traits.
Physicochemical and microbial properties of nanopowdered peanut sprout‐supplemented Caciocavallo‐like cheese during ripening
Authors: Ko Eun‐Jung , Chang Yoon Hyuk , Kwak Hae‐Soo 
Published: September 2016

This study was carried out to investigate the physicochemical and microbial properties of nanopowdered peanut sprout‐supplemented Caciocavallo‐like cheese (NPSCC) during ripening at 14 °C for 6 weeks. The total phenol contents and lactic acid bacteria counts in NPSCC were significantly higher than those in the control, indicating that nanopowdered peanut sprout could potentially be used as a prebiotic and potential source of dietary antioxidants in the dairy products. Thiobarbituric acid values of the cheese were significantly decreased and the production of short‐chain free fatty was not significantly different when nanopowdered peanut sprout was added into the production of Caciocavallo‐like cheese.
A randomised controlled trial of paracetamol and ibuprofen with or without codeine or oxycodone as initial analgesia for adults with moderate pain from limb injury
Authors: Graudins Andis , Meek Robert , Parkinson Jacqueline , Egerton‐Warburton Diana , Meyer Alastair 
Published: September 2016

AbstractObjectiveCompare pain relief from non‐opioid, codeine and oxycodone analgesic regimens in adults with moderate pain from limb injury.MethodDouble‐blind, randomised, controlled, non‐inferiority trial. Three regimens of six tablets, each included 2 × 500 mg paracetamol and 2 × 200 mg ibuprofen with 2 × 100 mg thiamine (non‐opioid), 2 × 30 mg codeine (codeine) or 2 × 5 mg oxycodone tablets (oxycodone). Primary outcome: difference in mean visual analogue scale (VAS) change between groups at 30 min, with a limit of inferiority of 13. Secondary outcomes included mean change in VAS rating from baseline to 30 min for each group, patient satisfaction, need for additional analgesia and adverse events. Pain ratings taken at 60 and 90 min for patients still in ED are described.ResultsOf 182 patients randomised, non‐opioid, codeine and oxycodone numbers were 61, 62 and 59. Differences (95% CI) between groups at 30 min were as follows: non‐opioid versus codeine −2.6 (−8.8 to 3.6); non‐opioid versus oxycodone −2.7 (−9.3 to 3.9); codeine versus oxycodone 0.1 (−6.6 to 6.4). Mean VAS reductions for non‐opioid, codeine and oxycodone were −13.5, −16.1 and −16.2 mm, respectively. Satisfaction with analgesia was reported by 77.6% (64.7–87.5), 81.0% (67.2–89.0) and 73.6% (59.7–84.7) and adverse events by 3.3% (0.4–11.3), 1.6% (0.4–8.7) and 16.9% (8.4–29.0), respectively. Mean VAS reductions at 60 and 90 min were as follows: −23.2 and −18.7 mm for non‐opioid; −30.7 and −33.3 mm for codeine; and −26.1 and −31.7 mm for oxycodone.ConclusionAt 30 min, analgesic effects of non‐opioid, codeine and oxycodone groups were non‐inferior.
Lycopene: Heterogeneous Catalytic E/Z Isomerization and In Vitro Bioaccessibility Assessment Using a Diffusion Model
Authors: Sun Qingrui , Yang Cheng , Li Jing , Raza Husnain , Zhang Lianfu 
Published: September 2016

AbstractHighly efficient heterogeneous catalytic E/Z isomerization of lycopene was achieved using an iodine‐doped titanium dioxide (I‐TiO2) catalyst prepared by sol‐gel method. The effects of reaction temperature and reaction time were investigated in detail. The maximum total Z‐ratio of lycopene exceeded 78% after 2 h of refluxing at 75 °C in ethyl acetate. Moreover, lycopene samples with a series of total Z‐ratios were prepared and the bioaccessibility of these samples was estimated using a diffusion model, the results showed that the bioaccessibility of lycopene markedly increased conforming to a linear regression model with increasing of the total Z‐ratio of lycopene from 3.6% to 78.5%. Furthermore, the specific role of the microstructure and melting point of 3.6% and 78.5% total Z‐ratio of lycopene was also investigated to understand the probable mechanism for the enhanced bioaccessbility of (Z)‐lycopenes.
Identification of the Critical Amino Acid Residues of Immunoglobulin E and Immunoglobulin G Epitopes in α‐Lactalbumin by Alanine Scanning Analysis
Authors: Yanjun Cong , Shengyun Zhou , Linfeng Li 
Published: September 2016

Abstractα‐Lactalbumin represents one of the major allergens causing cow milk allergy. Few studies have clearly evaluated immunological relationships between immunoglobulin E (IgE) and immunoglobulin G (IgG)‐binding epitopes of α‐lactalbumin. IgE‐ and IgG‐binding epitopes were immunolabeled with individual sera from cow milk‐allergic patients. Alanine scanning of immunodominant epitopes was used to identify the critical amino acid (aa). Our initial data revealed Val8, Phe9, Arg10, Tyr103, Leu105, and His107 were the critical aa for IgE‐binding epitope. The critical aa of IgG‐binding epitopes were Phe9, Leu15, Pro24, Trp26, and His32. This study will provide necessary information to alter the cDNA to encode a protein capable of activating milk‐specific T cells, but with reduced IgE‐ or IgG‐binding capacity.
Continental‐Scale River Flow Modeling of the Mississippi River Basin Using High‐Resolution NHDPlus Dataset
Authors: Tavakoly Ahmad A. , Snow Alan D. , David Cédric H. , Follum Michael L. , Maidment David R. , Yang Zong‐Liang 
Published: September 2016

AbstractAs a key component of the National Flood Interoperability Experiment (NFIE), this article presents the continental scale river flow modeling of the Mississippi River Basin (MRB), using high‐resolution river data from NHDPlus. The Routing Application for Parallel computatIon of Discharge (RAPID) was applied to the MRB with more than 1.2 million river reaches for a 10‐year study (2005‐2014). Runoff data from the Variable Infiltration Capacity (VIC) model was used as input to RAPID. This article investigates the effect of topography on RAPID performance, the differences between the VIC‐RAPID streamflow simulations in the HUC‐2 regions of the MRB, and the impact of major dams on the streamflow simulations. The model performance improved when initial parameter values, especially the Muskingum K parameter, were estimated by taking topography into account. The statistical summary indicates the RAPID model performs better in the Ohio and Tennessee Regions and the Upper and Lower Mississippi River Regions in comparison to the western part of the MRB, due to the better performance of the VIC model. The model accuracy also increases when lakes and reservoirs are considered in the modeling framework. In general, results show the VIC‐RAPID streamflow simulation is satisfactory at the continental scale of the MRB.