bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular epidemiology of Escherichia coli producing CTX-M and plasmid AmpC-type β-lactamases from dairy farms identifies a dominant plasmid encoding CTX-M-32 but no evidence for transmission to humans in the same geographical region
Authors: Findlay Jacqueline , Mounsey Oliver , Lee Winnie W.Y. , Newbold Nerissa , Morley Katy , Schubert Hannah , Gould Virginia C. , Cogan Tristan A. , Reyher Kristen K. , Avison Matthew B. 
Published: November 2019

AbstractThird-generation cephalosporin resistance (3GC-R) in Escherichia coli is a rising problem in human and farmed animal populations. We conducted whole genome sequencing analysis of 138 representative 3GC-R isolates previously collected from dairy farms in South West England and confirmed by PCR to carry acquired 3GC-R genes. This analysis identified blaCTX-M (131 isolates: encoding CTX-M-1, −14, −15, −32 and the novel variant, CTX-M-214), blaCMY-2 (6 isolates) and blaDHA-1 (one isolate). A highly conserved plasmid was identified in 73 isolates, representing 27 E. coli sequence types. This novel ~220 kb IncHI2 plasmid carrying blaCTX-M-32 was sequenced to closure and designated pMOO-32. It was found experimentally to be stable in cattle and human transconjugant E. coli even in the absence of selective pressure and was found by multiplex PCR to be present on 26 study farms representing a remarkable range of transmission over 1500 square kilometres. However, the plasmid was not found amongst human urinary E. coli we have recently characterised from people living in the same geographical location, collected in parallel with farm sampling. There were close relatives of two blaCTX-M plasmids circulating amongst eight human and two cattle isolates, and a closely related blaCMY-2 plasmid found in one cattle and one human isolate. However, phylogenetic evidence of recent sharing of 3GC-R strains between farms and humans in the same region was not found.ImportanceThird-generation cephalosporins (3GCs) are critically important antibacterials and 3GC-resistance (3GC-R) threatens human health, particularly in the context of opportunistic pathogens such as Escherichia coli. There is some evidence for zoonotic transmission of 3GC-R E. coli through food, but little work has been done examining possible transmission (e.g. via interaction of people with the local near-farm environment). We characterised acquired 3GC-R E. coli found on dairy farms in a geographically restricted region of the United Kingdom and compared these with E. coli from people living in the same region, collected in parallel. Whilst there is strong evidence for recent farm-to-farm transmission of 3GC-R strains and plasmids – including one epidemic plasmid that has a remarkable capacity to transmit – there was no evidence that 3GC-R found on study farms had a significant impact on circulating 3GC-R E. coli strains or plasmids in the local human population.
Recombination and selection against introgressed DNA
Authors: Veller Carl , Edelman Nathaniel B. , Muralidhar Pavitra , Nowak Martin A. 
Published: November 2019

AbstractDNA introgressed from one species into another is typically deleterious at many genomic loci in the recipient species. It is therefore purged by selection over time. Here, we use mathematical modeling and whole-genome simulations to study the influence of recombination on the purging of introgressed DNA. We find that aggregate recombination controls the genome-wide rate of purging in the first few generations after admixture, when purging is most rapid. Aggregate recombination is quantified by, the average recombination rate across all locus pairs, and analogous metrics. It is influenced by the number of crossovers (i.e., the map length) and their locations along chromosomes, and by the number of chromosomes and heterogeneity in their size. A comparative prediction of our analysis is that species with fewer chromosomes should purge introgressed DNA more profoundly, and therefore should exhibit a weaker genomic signal of historical introgression. With regard to patterns across the genome, we show that, in heterogametic species with autosomal recombination in both sexes, more purging is expected on sex chromosomes than on autosomes, all else equal. The opposite prediction holds for species without autosomal recombination in the heterogametic sex. Finally, we show that positive genomic correlations between local recombination rate and introgressed ancestry, as recently observed in several taxa, are likely driven not by recombination’s effect in unlinking neutral from deleterious introgressed alleles, but rather by its effect on the rate of purging of the deleterious alleles themselves.Note on this versionAn earlier version of this manuscript had two parts: (1) Calculations of the variance of genetic relatedness between individuals with particular pedigree relationships, taking into account the randomness of recombination and segregation in their pedigree. (2) An investigation of the rate of purging of introgressed DNA following admixture, based in part on results from part (1). Part (1) has since been published as Veller et al. (2020). The present manuscript has been reconfigured to focus on part (2).
Individual kinetochore-fibers locally dissipate force to maintain robust mammalian spindle structure
Authors: Long Alexandra F. , Suresh Pooja , Dumont Sophie 
Published: November 2019

AbstractAt cell division, the mammalian kinetochore binds many spindle microtubules that make up the kinetochore-fiber. To segregate chromosomes, the kinetochore-fiber must be dynamic and generate and respond to force. Yet, how it remodels under force remains poorly understood. Kinetochore-fibers cannot be reconstitutedin vitro, and exerting controlled forcesin vivoremains challenging. Here, we use microneedles to pull on mammalian kinetochore-fibers and probe how sustained force regulates their dynamics and structure. We show that force lengthens kinetochore-fibers by persistently favoring plus-end polymerization, not by increasing polymerization rate. We demonstrate that force suppresses depolymerization at both plus- and minus-ends, rather than sliding microtubules within the kinetochore-fiber. Finally, we observe that kinetochore-fibers break but do not detach from kinetochores or poles. Together, this work suggests an engineering principle for spindle structural homeostasis: different physical mechanisms of local force dissipation by the k-fiber limit force transmission to preserve robust spindle structure. These findings may inform how other dynamic, force-generating cellular machines achieve mechanical robustness.
Improved protein structure prediction using predicted inter-residue orientations
Authors: Yang Jianyi , Anishchenko Ivan , Park Hahnbeom , Peng Zhenling , Ovchinnikov Sergey , Baker David 
Published: November 2019

AbstractThe prediction of inter-residue contacts and distances from co-evolutionary data using deep learning has considerably advanced protein structure prediction. Here we build on these advances by developing a deep residual network for predicting inter-residue orientations in addition to distances, and a Rosetta constrained energy minimization protocol for rapidly and accurately generating structure models guided by these restraints. In benchmark tests on CASP13 and CAMEO derived sets, the method outperforms all previously described structure prediction methods. Although trained entirely on native proteins, the network consistently assigns higher probability tode novodesigned proteins, identifying the key fold determining residues and providing an independent quantitative measure of the “ideality” of a protein structure. The method promises to be useful for a broad range of protein structure prediction and design problems.
Enhanced representation of natural sound sequences in the ventral auditory midbrain
Authors: González-Palomares Eugenia , López-Jury Luciana , García-Rosales Francisco , Hechavarria Julio C. 
Published: November 2019

SummaryThe auditory midbrain (inferior colliculus, IC) plays an important role in sound processing, acting as hub for acoustic information extraction and for the implementation of fast audio-motor behaviors. IC neurons are topographically organized according to their sound frequency preference: dorsal IC regions encode low frequencies while ventral areas respond best to high frequencies, a type of sensory map defined as tonotopy. Tonotopic maps have been studied extensively using artificial stimuli (pure tones) but our knowledge of how these maps represent information about sequences of natural, spectro-temporally rich sounds is sparse. We studied this question by conducting simultaneous extracellular recordings across IC depths in awake bats (Carollia perspicillata) that listened to sequences of natural communication and echolocation sounds. The hypothesis was that information about these two types of sound streams is represented at different IC depths since they exhibit large differences in spectral composition, i.e. echolocation covers the high frequency portion of the bat soundscape (> 45 kHz), while communication sounds are broadband and carry most power at low frequencies (20-25 kHz). Our results showed that mutual information between neuronal responses and acoustic stimuli, as well as response redundancy in pairs of neurons recorded simultaneously, increase exponentially with IC depth. The latter occurs regardless of the sound type presented to the bats (echolocation or communication). Taken together, our results indicate the existence of mutual information and redundancy maps at the midbrain level whose response cannot be predicted based on the frequency composition of natural sounds and classic neuronal tuning curves.
Organisational embeddedness as a moderator on the organisational support, trust and workplace deviance relationships
Authors: Singh Riann 
Published: November 2019

PurposeEmerging research calls for the exploration of the potential negative side of organisational embeddedness. It is important to assess such negative aspects to fully understand the power of embeddedness, and how to address the potential undesirable effects on employees and organisations. The purpose of this paper is to answer this call by assessing the extent to which organisational embeddedness can negatively influence the perceived organisational support-workplace deviance and the organisational trust–deviance relationships.Design/methodology/approachA sample of 969 employees across the financial services sector in the Caribbean nation of Trinidad is used, with a two-wave research design. Multiple hierarchical regression analysis is used to test the research relationships.FindingsThe findings support the propositions that organisational support and trust each negatively predicts workplace deviance and organisational embeddedness moderates each of these relationships in an undesirable way, such that, higher embeddedness weakens the desirable relationships between support, trust and deviance.Originality/valueThis study addresses a clear gap since limited studies explore the potential negative impact of organisational embeddedness on various work perceptions and behaviours. Embeddedness is largely considered a predictor of various desirable employee and organisational outcomes.
Time–cost–quality trade-off analysis for planning construction projects
Authors: Wang Tianqi , Abdallah Moatassem , Clevenger Caroline , Monghasemi Shahryar 
Published: November 2019

PurposeAchieving project objectives in constructionprojects such as time, cost and quality is a challenging task. Minimizing project cost often results in additional project duration and might jeopardize quality, and minimizing project duration often results in additional cost and might jeopardize quality. Also, increasing construction quality often results in additional cost and time. The purpose of this paper is to identify and analyze trade-offs among the project objectives of time, cost and quality.Design/methodology/approachThe optimization model adopted a quantitative research method and is developed in two main steps formulation step that focuses on identifying model decision variables and formulating objective functions, and implementation step that executes the model computations using multi-objective optimization of Non-Dominated Sorting Genetic Algorithms to identify the aforementioned trade-offs, and codes the model using python. The model performance is verified and tested using a case study of construction project consisting of 20 activities.FindingsThe model was able to show practical and needed value for construction managers by identifying various trade-off solutions between the project objectives of time, cost and quality. For example, the model was able to identify the shortest project duration at 84 days while keeping cost under $440,000 and quality higher than 85 percent. However, with an additional budget of $20,000 (4.5 percent increase), the quality can be increased to 0.935 (8.5 percent improvement).Research limitations/implicationsThe present research work is limited to project objectives of time, cost and quality. Future expansion of the model will focus on additional project objectives such as safety and sustainability. Furthermore, new optimization models can be developed for construction projects with repetitive nature such as roads, tunnels and high rise buildings.Practical implicationsThe present model advances existing research in planning construction projects efficiently and achieving important project objectives. On the practical side, the optimization model will support the construction industry by allowing construction managers to identify the highest quality to deliver a construction project within specified budget and duration, lowest cost for specified duration and quality or shortest duration for specified budget and quality.Originality/valueThe present model introduces new and innovative method of increasing working hours per day and number of working days per shift while analyzing labor working efficiency and overtime rate to identify optimal trade-offs among important project objectives of time, cost and quality.
Friction factor calculation for turbulent flow in annulus with temperature effects
Authors: Sorgun Mehmet , Ulker Erman 
Published: November 2019

Purpose
The purpose of this paper is to present a new friction factor equation for practical use, including fluid temperature, pipe diameter ratio and inner pipe rotation effects.

Design/methodology/approach
A friction factor relationship is developed by applying Buckingham’s Theorem of dimensional analysis. Then, the formula is calibrated using experimental data conducted at Izmir Katip Celebi University flow loop. Moreover, the effects of fluid temperature, inner pipe rotation and pipe diameter ratio on friction factor are investigated experimentally.

Findings
Satisfactory agreements are obtained between proposed formula and experiments. The experimental results indicate that major variable parameters affecting friction factor is Reynolds number. Pipe rotation has negligible effect on friction factor at high Reynolds number. Prandtl number is one of the important parameters affecting the friction factor. Moreover, as the pipe diameter ratio is decreased, friction factor increases.

Originality/value
Determining fluid behavior of fluids under high temperature is especially important for deep wells during drilling. Temperature drastically changes fluid properties and flow characteristics in wells. These changes have a remarkable effect on pressure losses. However, since the temperature is considered constant in the calculation of the pressure loss, problems can be encountered in most systems. Friction factor is one of the important parameters for determining pressure loss in closed conduits. The originality of this work is to propose a new friction factor equation for practical use, including fluid temperature, pipe diameter ratio and inner pipe rotation effects.
Strategic alignment matrix
Authors: Bertolotti Fabiola , Macrì Diego Maria , Vignoli Matteo 
Published: November 2019

Purpose
This paper aims to proposes a framework, labeled strategic alignment matrix, to attain organizational alignment by integrating the horizontal dimension of performance (results driven by activities carried out by multiple organizational units) and the vertical one (results of single units) through the use of a sophisticated information structure composed by quantitative measures and management processes.

Design/methodology/approach
A science-based design approach was adopted. A review of the literature on strategic performance measurement systems (SPMS) and coordination allowed the identification of a set of design principles (guidelines reflecting the accumulated knowledge in the literature). The design principles guided the design of the proposed framework. The framework was tested in a tiles company on the new product development process.

Findings
Five design principles are presented for the design of a working SPMS as follows: to integrate the horizontal and vertical dimensions of performance; to have all the relevant information in one place (package); to understand how actors contribute to the overall performance; to favor the emergence of integrating conditions for coordination; and to enrich the role of quantitative non-financial information to attain inter-functional integration. During the test of the framework, managers highlighted the increased ability to coordinate actions and the existence of double-loop learning.

Research limitations/implications
The model was tested in one organization. The study should be replicated in other contexts connecting the strategic alignment matrix to the budgeting and incentive systems.

Originality/value
Working at the interface between science and design helps to address the theory-practice gap that has been a priority in management studies for long.
Economic convergence in the EU and Eurozone
Authors: Marelli Enrico Piero , Parisi Maria Laura , Signorelli Marcello 
Published: November 2019

Purpose
The purpose of this paper is to analyse whether several groups of European countries are on track for real “conditional” economic convergence in per capita income and the likely speed of convergence. The paper focusses also on the changes of the convergence processes over time.

Design/methodology/approach
Unlike the simple “absolute convergence”, it explores the concept of “conditional” or “club” convergence. Moreover, it adopts the approach of extending the univariate model to take into account the panel dimension over an extended time interval and endogeneity.

Findings
A process of real economic convergence has characterised the period under investigation (1995–2016), but, in general, the size and significance of the parameter is greater for the wide European Union (EU) area (EU25 and above) rather than the Eurozone (EZ). However, the crises occurred after 2008 caused most of such lower convergence in the Euro area.

Research limitations/implications
This paper gives an estimate of the speed/time needed to several groups of European countries (EZ, in particular) to achieve real economic convergence. Future research could further develop the “stochastic” convergence concept.

Originality/value
This is an analysis of convergence in enlarging EU and EZ for an extended period (including the big crisis period and the subsequent recovery). It shows that EZ experienced a drop in the speed of real convergence after 2008 and converge at lower speed than the EU. As a consequence, a specific budget for EZ would be important to provide adjustment mechanisms after potentially large shocks.
Does persistence in internationalization and innovation influence firms’ performance?
Authors: Iandolo Stefano , Ferragina Anna Maria 
Published: November 2019

Purpose
The purpose of this paper is to analyze the joint effect of persistency in innovation and export on firms’ total factor productivity. In particular, the aim is to determine if exporting in international markets along subsequent periods, and being also continuously innovating over the same periods, can be associated with increases in firms’ productivity. The underlying idea is that time recurrence of these strategies is related to the firms’ ability to optimize external knowledge flows enhancing their productivity.

Design/methodology/approach
By using data on Italian manufacturing firms over the period 1998–2006, the authors distinguish between repeated and temporary exporting firms, as well as repeated and temporary innovators, to test (through two-step system generalized methods of moments) the existence of any combined learning-by-exporting and learning-by-doing effects.

Findings
This paper provides empirical findings about persistent innovation efforts being better associated with a permanent presence in foreign markets. More in detail, persistently innovative and exporting firms have better productivity results than persistently exporting (innovating) firms with non-persistent innovation (export). Combining both strategies could be an opportunity to internalize knowledge flows coming from long-lasting exposure to foreign markets. These results hold especially for small firms.

Originality/value
The novelty of this paper is twofold. First, the authors argue that the temporal dimension of firms’ exporting and innovating activities may influence firms’ productivity. Second, while previous studies explored the role of export and innovation on productivity in isolation, the authors consider the joint effect of this relationship and also explore it across the temporal dimension finding evidence that they have a positive, reinforced effects if firms implement these activities continuously and jointly. In this case, the effect of innovation and export on productivity is significantly higher than if firms with intermittent strategies do not have the time to internalize knowledge flows coming from participating in export market.
Tourism and social media in the world: an empirical investigation
Authors: Asongu Simplice , Odhiambo Nicholas M. 
Published: November 2019

Purpose
The purpose of this paper is to examine the relationship between tourism and social media from a cross section of 138 countries with data for the year 2012.

Design/methodology/approach
The empirical evidence is based on Ordinary Least Squares, Negative Binomial and Quantile Regressions.

Findings
Two main findings are established. First, there is a positive relationship between Facebook penetration and the number of tourist arrivals. Second, Facebook penetration is more relevant in promoting tourist arrivals in countries where initial levels in tourist arrivals are the highest and low. The established positive relationship can be elucidated from four principal angles: the transformation of travel research, the rise in social sharing, improvements in customer service and the reshaping of travel agencies.

Originality/value
This study explores a new data set on social media. There are very few empirical studies on the relevance of social media in development outcomes.