bluuebunny/crossref_metadata_2025_split huggingface dataset:
Best practices for genome-wide RNA structure analysis: combination of mutational profiles and drop-off information
Authors: Novoa Eva Maria , Beaudoin Jean-Denis , Giraldez Antonio J , Mattick John S , Kellis Manolis 
Published: August 2017

ABSTRACTGenome-wide RNA structure maps have recently become available through the coupling ofin vivochemical probing reagents with next-generation sequencing. Initial analyses relied on the identification of truncated reverse transcription reads to identify the chemically modified nucleotides, but recent studies have shown that mutational signatures can also be used. While these two methods have been employed interchangeably, here we show that they actually provide complementary information. Consequently, analyses using exclusively one of the two methodologies may disregard a significant portion of the structural information. We also show that the identity and sequence environment of the modified nucleotide greatly affect the odds of introducing a mismatch or causing reverse transcriptase drop-off. Finally, we identify specific mismatch signatures generated by dimethyl sulfate probing that can be exploited to remove false positives typically produced in RNA structurome analyses, and how these signatures vary depending on the reverse transcription enzyme used.
Metagenomic sequencing to replace semi-quantitative urine culture for detection of urinary tract infections: a proof of concept
Authors: Janes Victoria A. , Matamoros Sébastien , Willemse Niels , Visser Caroline E. , Wever Bob de , Jakobs Marja E. , Subramanian Poorani , Hasan Nur A. , Colwell Rita R. , de Jong Menno D. , Schultsz Constance 
Published: August 2017

ABSTRACTSemi-quantitative bacterial culture is the standard method to diagnose urinary tract infections (UTI), but bacterial growth rate limits diagnostic speed and it is unreliable when patients have been pre-treated with antibiotics. Metagenomics could increase diagnostic speed and accuracy by sequencing the microbiome and resistome directly from urine samples, bypassing culture. However, a semi-quantitative approach – as needed for diagnosing UTIs – has not been established.Metagenomics was deployed to identify and semi-quantify bacterial presence indicative of UTI, predict antimicrobial susceptibility (AMR), and results were compared to semi-quantitative culture. Whole genome sequencing of the corresponding uropathogens was done for comparison. Analysis time and cost were tracked.Forty-one consecutive urine samples underwent metagenomic analysis. All culture positive samples contained >200ng of DNA, suggestive of a threshold below which UTI could be ruled out solely based on DNA quantity. A semi-quantitative Diagnostic Index (DI) was created by multiplying the total DNA quantity by the relative abundance of uropathogens per urine sample. The DI allowed discrimination of UTI from non-UTI samples in all but 1 case. Metagenomic detection of AMR determinants correctly predicted the phenotype of uropathogens in 20 of 32 cases. The metagenomic work-flow was 31h and cost €116 per sample, but could be reduced to 4.5h and €5 for low-DNA-yield non-UTI samples.The genomic determinants of AMR and their distribution across uropathogens need to be better understood for prediction of AMR phenotypes by metagenomics. The introduction of the DI demonstrates the potential of semi-quantitative metagenomics to replace culture as rapid diagnostic method for UTI.
Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress
Authors: Gasch Audrey P. , Yu Feiqiao Brian , Hose James , Escalante Leah E. , Place Mike , Bacher Rhonda , Kanbar Jad , Ciobanu Doina , Sandor Laura , Grigoriev Igor V. , Kendziorski Christina , Quake Stephen R. , McClean Megan N. 
Published: August 2017

ABSTRACTFrom bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing to quantify transcript heterogeneity in singleS. cerevisiaecells treated with and without salt stress, to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. We also discovered that a subset of cells decouple expression of ribosomal protein genes from the environmental stress response, in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results reveal that cells maintain a cellular filter against decoupled bursts of transcription-factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells.
A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid
Authors: Ponce-de-Leon Miguel , Tamarit Daniel , Calle-Espinosa Jorge , Mori Matteo , Latorre Amparo , Montero Francisco , Pereto Juli 
Published: August 2017

AbstractBacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism –which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphidCinara cedrithat harbors two co-primary endosymbionts,Buchnera aphidicolaBCc andCa.Serratia symbiotica SCc, and in which some metabolic pathways are partitioned between different partners. Here we present a genome scale metabolic network (GEM) for the bacterial consortium from the cedar aphidiBSCc. The analysis of this GEM allows us the confirmation of cases of metabolic complementation previously described by genome analysis (i.e. tryptophan and biotin biosynthesis) and the proposal of a hitherto unnoticed event of metabolic pathway sharing between the two endosymbionts, namely the biosynthesis of tetrahydrofolate.In silicoknock-out experiments withiBSCc showed that the consortium metabolism is a highly integrated yet fragile network. We also have explored the evolutionary pathways leading to the emergence of metabolic complementation between reduced metabolisms starting from individual, complete networks. Our results suggest that, during the establishment of metabolic complementation in endosymbionts, adaptive evolution is more significant than previously thought.
Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach
Authors: Jacobs A. , De Noia M. , Praebel K. , Kanstad-Hanssen Ø , Paterno M. , Jackson D. , McGinnity P. , Sturm A. , Elmer KR , Llewellyn MS 
Published: August 2017

AbstractCaligid sea lice represent a significant threat to salmonid aquaculture worldwide.Lepeophtheirus salmonisis the predominant species that occurs in the Northern Hemisphere. Dispersal of sea lice between marine aquaculture sites and geographic regions is thought to occur rapidly via planktonic transport of larvae. Population genetic analyses have consistently shown minimal population genetic structure in North AtlanticL. salmonis, frustrating efforts to track louse populations, improve targeted control measures and understand local adaption to environmental conditions. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among fourL. salmonispopulations from Ireland (N=2, 27 individuals), Scotland (N=1, 11 individuals) and North Norway (N=1, 12 individuals). Weak global structure (FSC= 0.018, p<0.0001) and only one significant pairwise FSTcomparison was observed (Scotland vs Kenmare Bay, (FST= 0.018, p<0.0001)) using all 1286 SNPs. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment (DAPC assignment probability = 1), increased global Fsc= 0.098, (p<0.0001) and resulted in pairwise comparisons that all showed highly significant Fst-values (range = 0.081 – 0.096, p<0.0001). Out of 19 SNPs found to be under directional selection between populations, 12 corresponded to the discriminatory SNPs identified using random forest. Taken together our data suggest thatL. salmonisSNP diversity exists with which it is possible to discriminate differences between nearby populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.
Effect of ligands on stability of H-Ras GTPase
Authors: Kovrigina Elizaveta A , O’Connor Casey , Kovrigin Evgenii L 
Published: August 2017

ABSTRACTThe G domain of a small monomeric GTPase Ras contains a nucleotide-binding pocket and a magnesium-binding site essential for the Ras function in cellular signaling. The G domain also has another (allosteric) ion-binding site on the rear surface of the G domain, which function is still unknown. In this paper, we detailed the effect of calcium and magnesium ions on stability of Ras bound to GDP, GTP, and GTP-mimic GppNHp. We revealed that the remote allosteric ion-binding site contributes very significantly to stability of Ras in the GDP-bound conformation, but nearly not at all—when Ras is bound to a GTP mimic. These findings highlight that further studies of the remote ion-binding site are warranted to reveal its role in the Ras function.
Co-creating value and developing social capital: Centre of Science for Villages (CSV), Wardha
Authors: Shukre Anagha , Verma Naresh 
Published: August 2017

Subject area
Marketing management, consumer behaviour, rural marketing and integrated marketing communications.

Study level/applicability
The case is for the use of undergraduate and also postgraduate students of management in courses of marketing management, consumer behaviour, rural marketing and integrated marketing communications. This case may also be used in human resources’ management course lectures which focus on social capital.

Case overview
This case on the Centre of Science for Villages (CSV), Wardha, attempts to identify how value can be co-created through innovative technology and how social capital can be developed for rural markets through the use of integrated marketing communications tools, particularly word-of-mouth and the influence of opinion leaders. Effective campaigns can be designed for the target audience based on the 3A framework (Awareness, Adoption and Addition of Value) and McGuire’s Model of Persuasion. The CSV has been typically chosen for the study because its products are unique, innovative and eco-friendly and blend well with the rural lives. It has been able to enrich the lives of rural population by generating employment and in creating entrepreneurial opportunities. The biggest challenge, however, lies in educating rural consumers to accept and adopt its innovative technology in their daily lives.

Expected learning outcomes
The case study has been written to enable students to understand the concepts of value co-creation and social capital in the context of Indian rural markets. The students will learn the dynamics of rural markets by pondering over these points: understand the concept of value co-creation for rural markets; comprehend the creation of social ecology for managing knowledge in an organisation; identify the development and role of social capital and use it as a promotional tool, particularly word-of-mouth and opinion leaders(reference groups); recommend the use of different marketing mix variables for an organisation, operating in rural markets; and connote designing of effective campaigns for the target audience, based on the 3A framework and the Persuasion Model (6 steps) suggested by McGuire.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 8: Marketing
Valuating and analyzing the patent portfolio: the patent portfolio value index
Authors: Grimaldi Michele , Cricelli Livio , Rogo Francesco 
Published: August 2017

Purpose
The purpose of the paper is to advance a framework that can assess and analyze the value of patent portfolios. On this purpose, the framework develops a conceptual and comprehensive index, the patent portfolio value index (PPVI), to assess the patent innovation level and suggest economic-strategic guidelines.

Design/methodology/approach
The authors have designed and applied a framework that synthesizes into a single index the results of a multiple criteria approach, based on information derived from quantitative objective data (claims, citations, and market coverage), information related to qualitative determinants (strategic positioning and economic importance), and information derived from decision makers’ perceptions and judgments.

Findings
The authors have applied the PPVI to the 3,532 patent portfolio documents in an Italian worldwide player in aerospace and defense market. The combined analysis, provided by the PPVI and a qualitative synoptic representation, has made it possible to understand the strategic positioning and alignment of patents with the core business of the company. The results of the analysis have provided managers with the necessary suggestions regarding action items to be performed: to reinforce, license, try to dismiss, or sell some of the examined patents of the portfolios.

Practical implications
The PPVI supplies a quick procedure to ascertain the profitability of patents and accounts for the value of a patent portfolio from an internal business perspective.

Originality/value
As it is built and defined, the PPVI shows elements of novelty compared to the other indexes existing in the literature, in that it follows a multiple criteria approach by merging quantitative and qualitative information.
Business cycle and investment flows of retail and institutional mutual funds
Authors: Salganik-Shoshan Galla 
Published: August 2017

PurposeThe purpose of this paper is to investigate the dynamics of mutual fund investment flows across the business cycle. To account for the differences in the flow patterns of funds catered for institutional investors and those focusing on retail investors, the author conducts this investigation separately for flows of institutional and retail funds.Design/methodology/approachThe author uses the sample of US equity mutual funds for the period between 1999 and 2012. For the samples of each type of fund, the author performs separate analyses for expansion and recession periods. Following Sirri and Tufano (1998), the author implements the Fama MacBeth (1973) approach.FindingsThe author finds that flow patterns of both fund types vary across the business cycle. For example, the results reveal that during bad times, institutional investors demonstrate weaker return-chasing behavior, while paying higher attention to Jensen’sα, than during good times. In addition, the author reports results on the effect of fund exposure to various systematic risk factors. For instance, the author observes that during economic downturns, investors of both fund types tend to punish managers with higher market exposure. During expansions, the fund’s market exposure positively affects flows of institutional funds, while its effect on the flows of retail funds remains negative.Originality/valueTo the best of the author’s knowledge, this is the first study that investigates mutual fund investment flow patterns across the business cycle, while simultaneously accounting for differences in flow patterns between retail and institutional funds. A further contribution of this paper is that it explores the previously overlooked relationships between fund flows and their exposure to various systematic risk factors.
Quantitative appraisal of cost and time performance of construction projects in public and private universities in Osun State, Nigeria
Authors: Olatunde Nathaniel Ayinde , Alao Oluwaseyi Olalekan 
Published: August 2017

Purpose
The purpose of this paper is to compare the cost and time performance of construction projects in public and private universities in Osun State, Nigeria.

Design/methodology/approach
Purposive sampling technique was adopted to select four universities (two public and two private) used for the study. Archival data on 40 completed construction projects (ten from each university) was used in the study. Data were analysed with percentile and t-test.

Findings
The study showed that only 35 per cent of the construction projects in public and 10 per cent of those in private universities were completed at the estimated cost. There were no construction projects completed within the planned time in public universities, but 20 per cent were completed within the planned time in private universities. The t-test showed there is no significant difference in performance of construction projects in public and private universities in Nigeria. The study concluded that time performance of public and private universities in Nigeria was still below acceptable international best practices.

Research limitations/implications
The findings of this study are limited to universities’ construction projects and may be of little application to other construction projects outside university settings.

Practical implications
It is recommended that construction stakeholders be more proactive in ensuring that significant improvement is achieved in cost and time performance of construction projects both in public and private universities; the clients need to be more detailed in their briefs and requirements, the designers (architects and engineers) need to be more precise and avoid varying their designs, the quantity surveyors should use their professional competency in cost engineering adequately and the contractor should avoid spurious claims that result in increase in construction cost and time so that performance of construction projects can be improved.

Originality/value
The study is an attempt to compare cost and time performance of construction projects in public and private universities in Osun State, Nigeria.
Identifying path-breaking transitions for Kenya’s marginalised communities in water and sanitation provision
Authors: Maina Wairimu , van Graan Andre 
Published: August 2017

Purpose
This paper aims to illustrate relationships between stakeholders in the conceptualisation and implementation of water and sanitation services (WSS) projects in marginalised settings of Nairobi and Kiambu Counties. It outlines these relationships in a flow diagram that shows a pathway analysis in which social innovation strategies are used as markers in the program of inclusive water provision. The study’s objective is to map the processes of social innovation in an effort to highlight the role of marginalised communities in their access to the right to water.

Design/methodology/approach
The paper approached the study using a case study design, and thereafter, constructivist grounded theory was used to further delve into the comparative cases. To map the processes of social innovation, the case study design was seen to be appropriate, as it sequenced activities in a time-series analysis. From these two case studies, four comparative cases were used to pinpoint path-breaking transition in the pathway analysis. The methods used in both phases were, namely, in-depth interviews, observations and document analysis, and these were complemented by field notes.

Findings
The paper indicates an opportunity to use emergent patterns for a more context-specific analysis of WSS projects in marginalised communities. It advances the role of marginalised communities as vital stakeholders in the approach described as “the right to the city”. The model of spatial appropriation brings to the fore the binary yet separate processes that stakeholders engage in.

Research limitations/implications
Owing to the use of a grounded theory model, the results may not be transferable to other contexts. Therefore, further testing of the proposed pathway analysis and model is encouraged, as this model suggests ways of ensuring full community engagement which would result in greater success in projects involving marginalised communities.

Practical implications
The paper has implications for both the government and communities, in that more deliberate roles for the community-based organisation in the conceptualisation of WSS projects can lead to social learning opportunities for government institutions and greater success in implementation.

Originality/value
The paper justifies the need for government institutions to map and evaluate WSS projects using emergent patterns to highlight the role of marginalised communities as their right to the city.
The development of a theoretical framework of organisational rhythm
Authors: Poels Truus , Tucker Danielle A. , Kielema Joop 
Published: August 2017

PurposeThe purpose of this paper is to develop a framework to understand organisational rhythm as a stimulus for further study into organisational change.Design/methodology/approachThis paper studies the experiences of the medical discipline colleges in the Netherlands as they underwent significant reorganisation and transfer of ministerial authority. The data set consists of correspondence, reports and tapes of the meetings over 14 months and interviews with 26 employees.FindingsThis research identified five sub-themes of rhythm (emphasis, intonation, pace, period and repetition). Putting these together, the authors present a framework to understand organisational rhythm during organisational change.Research limitations/implicationsThis study begins to develop understanding of how rhythms function but the authors did not compare multiple rhythms in this study.Practical implicationsThe authors argue that by unpacking and exploring in more detail the sub-themes of rhythm (emphasis, intonation, pace, period and repetition), the authors can help to explain why complex change management initiatives may stall or fail to gain traction. By understanding the concept of rhythm as movement, the authors can offer recommendations to organisations about how to move forward and overcome challenges associated with progress.Originality/valueIn this paper, the authors make an important distinction between rhythm in terms of movement and flow of activity, which has often been overlooked by research, which focusses on the temporal aspects of organisations, which the authors classify as frequency – relating to the sequencing and duration of change.