bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal Denaturation of DNA G-Quadruplexes and their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry
Authors: Marchand Adrien , Rosu Frédéric , Zenobi Renato , Gabelica Valérie 
Published: July 2018

ABSTRACTAs the idea that G-quadruplex nucleic acid structures are involved in cellular processes is gaining support, it becomes important to develop ligands that specifically target G-quadruplexes. However, ligand design is complicated because there are multiple G-quadruplex target sequences, some sequences are polymorphic, and very few ligand-quadruplex structures in solution were solved to date. Further, structure alone does not reveal the driving forces for ligand binding. To knowwhya ligand binds, the thermodynamics of binding must be characterized. Electrospray mass spectrometry makes it possible to detect and quantify each specific stoichiometry in terms of number of strands, number of specific cations, and number of ligands, and thus allows one to simultaneously determine the equilibrium constants for the formation of each complex. We designed and built a temperature-controlled nano-electrospray source to monitor thermal denaturation by mass spectrometry (“MS-melting”). We studied the thermal denaturation of G-quadruplexes, including the c-myc promoter and several telomeric sequence variants, and their complexes with popular ligands (Phen-DC3, TrisQ, TMPyP4, Cu-ttpy). From the temperature dependence of the equilibrium constants, we determined the enthalpic and entropic contributions to the formation of each stoichiometric state. In absence of ligand, we untangled the potassium-induced G-quadruplex folding thermodynamics, one potassium ion at a time. The formation of each quartet-K+-quartet units is strongly enthalpy driven, with entropy penalty. In contrast, the formation of quartet-K+-triplet units is entropically driven. For this reason, such misfolded structures can become more abundant as the temperature increases. In the presence of ligands, mass spectrometry also revealed new states at intermediate temperatures. For example, even in cases where only a 1:1 (ligand:quadruplex) is observed at room temperature, a 2:1 complex predominates at intermediate temperatures. Mass spectrometry also makes it easy to distinguish ligand bound to the 2-quartet structures (containing 1 K+), the 3-quartet structures (containing 2 K+) and to the unfolded strand (no specific K+). We confirm that TrisQ binds preferably, but not exclusively, to 3-quartet structures, Phen-DC3 binds to a 2-quartet structure, while the porphyrin ligand TMPyP4 is characterized as non-selective, because it binds to all forms including the unfolded one. The thermodynamics of ligand binding to each form, one ligand at a time, provides unprecedented detail on the interplay between ligand binding and changes in G-quadruplex topology.TOC Graphics
For common community phylogenetic analyses, go ahead and use synthesis phylogenies
Authors: Li Daijiang , Trotta Lauren , Marx Hannah E. , Allen Julie M. , Sun Miao , Soltis Douglas E. , Soltis Pamela S. , Guralnick Robert P. , Baiser Benjamin 
Published: July 2018

AbstractShould we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life [OTL]). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel’s λ and Blomberg’s K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman’s ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, were also highly correlated with estimates of Blomberg’s K or close to Pagel’s λ from purpose-built phylogenies when traits were simulated under Brownian Motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.
A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium
Authors: Steenwyk Jacob L. , Shen Xing-Xing , Lind Abigail L. , Goldman Gustavo H. , Rokas Antonis 
Published: July 2018

AbstractAbbreviations:NT, nucleotide; AA, amino acid; CI, credible interval; RCV, relative composition variability; IC, internode certainty; GSF, gene support frequencies; GLS, gene-wise log-likelihood scores; DVMC, degree of violation of a molecular clockThe filamentous fungal family Aspergillaceae contains > 1,000 known species, mostly in the genera Aspergillus and Penicillium. Several species are used in the food, biotechnology, and drug industries (e.g., Aspergillus oryzae, Penicillium camemberti), while others are dangerous human and plant pathogens (e.g., Aspergillus fumigatus, Penicillium digitatum). To infer a robust phylogeny and pinpoint poorly resolved branches and their likely underlying contributors, we used 81 genomes spanning the diversity of Aspergillus and Penicillium to construct a 1,668-gene data matrix. Phylogenies of the nucleotide and amino acid versions of this full data matrix as well as of five additional 834-gene data matrices constructed by subsampling the top 50% of genes according to different criteria associated with strong phylogenetic signal were generated using three different maximum likelihood schemes (i.e., gene-partitioned, unpartitioned, and coalescence). Examination of the topological agreement among these 36 phylogenies and measures of internode certainty identified 12 / 78 (15.4%) bipartitions that were incongruent and pinpoint the likely underlying contributing factors (incomplete lineage sorting, hybridization or introgression, and reconstruction artifacts associated with poor taxon sampling). Relaxed molecular clock analyses suggest that Aspergillaceae likely originated in the lower Cretaceous and the Aspergillus and Penicillium genera in the upper Cretaceous. Our results shed light on the ongoing debate on Aspergillus systematics and taxonomy and provide a robust evolutionary and temporal framework for comparative genomic analyses in Aspergillaceae. More broadly, our approach provides a general template for phylogenomic identification of resolved and contentious branches in densely genome-sequenced lineages across the tree of life.
The shadow price of nitrogen
Authors: Yang Ziyan 
Published: July 2018

PurposeThe most recent and prestigious scientific research shows that nitrogen leaching caused by over-used nitrogen fertilizer rapidly acidifies all soil types in China, revolutionizing the basic understanding of the mechanism of soil acidification. The purpose of this paper is to study the impact of nitrogen on soil acidity over the long run, which is the shadow price of nitrogen.Design/methodology/approachIn a discrete dynamic programming model, this paper compares the nitrogen application and soil pH between optimal nitrogen control that takes the shadow price of nitrogen into consideration and myopic nitrogen control that ignores that shadow price. Using a five-year panel experimental data on a rapeseed-rice rotation, this paper simulates and numerically solves the dynamic model.FindingsBoth theoretically and empirically, this paper shows that the over-use of nitrogen and the decline in soil pH are explained by ignorance of the shadow price of nitrogen. Compared with optimal nitrogen control, myopic nitrogen control applies more nitrogen in total, resulting in lower soil pH. In addition, over-use in the first season contributes to soil acidification and the carry-over effects mitigate that problem.Originality/valueThis paper enriches the literature by extending the study of the environmental impact of nitrogen leaching to its impact on the long-term loss in agricultural production, providing a new theoretical framework in which to study soil acidification rather than conventionally treating soil acidification as a secondary consequence of acid rain, and showing the possibility of using nitrogen control to mitigate soil acidification when lime applications are not feasible due to socio-economic constraints.
Understanding public opinion change of HPV vaccination controversy
Authors: Kim Sojung Claire , Namkoong Kang , Fung Timothy , Heo Kwangjun , Gunther Albert 
Published: July 2018

PurposeAlthough Human Papilloma Virus (HPV) is the most commonly diagnosed sexually transmitted infection in the USA, much controversy exists with respect to HPV vaccination, especially among parents of adolescents. Previous research has shown that exemplars in the media influence public opinion estimates about controversial social issues. However, little is known about the underlying psychological processes of how exemplars influence public opinion formation. The purpose of this paper is to systematically explore such psychological processes based on the projection theory. To this end, the important yet controversial public health issue, the mandatory HPV vaccination, was chosen.Design/methodology/approachA two-factor (exemplar vs proportion), between-subject experiment was conducted using online newspaper articles as main stimuli. A total of 138 participants completed the study. The analytical framework comprised the Sobel test with the Bootstrap method and a series of Ordinary Least Square hierarchical regression analyses.FindingsThe higher the proportion of exemplars against the HPV vaccination in a news article was, the greater the number of individuals who became opposed to it was. And the high personal opposition translated into negative public opinion change estimation.Originality/valueThe findings indicate that news exemplars may influence individuals’ personal opinion formation, and, in turn, contribute to their estimations of future public opinion climate, as suggested by the projection theory. Theoretical, methodological and practical implications for journalists, health educators and policy makers are discussed.
Critical review and analysis of measuring the success of Six Sigma implementation in manufacturing sector
Authors: Patel Mihir , Desai Darshak Arunbhai 
Published: July 2018

Purpose
The purpose of this paper is to capture the status of implementation of Six Sigma in various manufacturing industries and also examine the success of the Six Sigma by using different performance indicators.

Design/methodology/approach
The methodology of critical review involves the selection and classification of 112 research articles on the implementation of Six Sigma in different manufacturing industries. The selected articles are categorized by the following: articles distribution based on the year of publication, publication database, various journals, contribution of authors, continent, scale of industry, implemented approaches, focused industry, tools and techniques used in phases of Six Sigma methodology, and performance indicators used in Six Sigma implementation. Then after, future scopes of research opportunities are derived based on significant findings.

Findings
The literature revealed that: Very few work was undertaken on the implementation of Six Sigma in various manufacturing industries like ceramic, paper, gems and jewelry, cement, furniture, stone, fertilizer, forging, paper and surface treatment industries. Most of the researchers have considered very few performance indicators to identify the improvement after Six Sigma implementation. But, there is no clue regarding overall improvement in different perspectives after the implementation of Six Sigma. The financial indicators, personnel indicators, process indicators and customer indicators are useful to measure the overall improvement after the implementation of Six Sigma in the manufacturing sector.

Research limitations/implications
The study was carried out on the implementation of Six Sigma methodology in various manufacturing industries, and various performance indicators were identified while implementing the Six Sigma methodology. Case studies pertaining to service industries were not covered here.

Originality/value
Very little research has been carried out to measure the overall success of implementing Six Sigma methodology in manufacturing industries. This paper will provide value to students, researchers and practitioners of Six Sigma by providing insight into the implementation of Six Sigma in manufacturing industries.
Assessing relationship between quality management systems and business performance and its mediators
Authors: Bhatia Manjot Singh , Awasthi Anjali 
Published: July 2018

Purpose
The purpose of this paper is to examine the relationship between implementation of quality management systems (QMS) and business performance, through mediating factors (operating performance, information quality, product quality, design performance, environmental performance and competitive priorities). Most of the published literature examines the direct impact of implementation of QMS on business performance, and on some of the above stated factors. However, the impact of implementation of QMS on business performance, through these mediating factors has not received much attention. Accordingly, the authors develop a theoretical framework depicting impact of implementation of QMS on business performance through the above stated factors.

Design/methodology/approach
The paper proposes several hypotheses linking implementation of QMS, mediating factors and business performance. The hypothesized model is empirically tested using data collected from 120 professionals working in quality engineering/management in India and North America. The collected data are analyzed with the aid of structural equation modeling (SEM) technique.

Findings
Information quality and design performance have emerged as the important factors in the research. Information quality directly effects design performance, operating performance and environmental performance. The model indicates that besides a well-designed product, managers need to focus on the operating performance to improve overall product quality. Empirical evidence is found regarding direct and indirect effect of implementation of QMS on above stated mediating factors and on business performance.

Originality/value
The research fills a gap in the literature by considering several mediating factors that aid in improving business performance with implementation of QMS.
An empirical investigation of the Baldrige framework using applicant scoring data
Authors: Mai Feng , Ford Matthew W. , Evans James R. 
Published: July 2018

PurposeThe purpose of this paper is to overcome evaluative limitations of previous studies to provide a more decisive test of the causal relationships implied in the Baldrige Criteria for Performance Excellence (CPE) using a unique data source.Design/methodology/approachThe authors employ partial least squares path modeling on blinded scoring data from Baldrige Award applicants. In addition, the authors conduct multi-group analysis to examine whether the hypothesized causal model is universal across different industry sectors.FindingsThe path analysis provided strong support for the CPE framework in its entirety. However, analysis of sector-specific subsets of the data did not confirm all relationships, suggesting the possibility of industry-dependent performance excellence frameworks and raising new research questions to be explored.Practical implicationsThis research offers several pertinent implications for managers who seek to translate the theoretical CPE framework to actionable quality-improvement efforts.Originality/valueCPE operationalizes many total quality management (TQM) concepts and provides guidelines to TQM programs. This study validates the CPE framework using the most relevant data set to date – the applicant scoring data. The authors are also the first to investigate the cross-industry differences in the relationships between the CPE constructs.
The transformation of work in digitized public sector organizations
Authors: Plesner Ursula , Justesen Lise , Glerup Cecilie 
Published: July 2018

Purpose
The purpose of this paper is to examine what the authors can learn from organization studies of digital technologies and changes in public organizations, and to develop a research agenda that allows us to produce systematic knowledge about how work practices in the public sector change with digitization.

Design/methodology/approach
The paper is based on an analysis of the organizational studies literature on how digital technologies lead to changes in public sector organization. The literature comprises a wide range of different case studies, and they are analyzed with a specific focus on the insights they offer regarding bureaucracy, accountability and professionals.

Findings
The paper identifies various examples of how digital technologies change important aspects of public sector organizations relating to bureaucracy, accountability and professionals. It is a main finding that no systematic account exists in the organization literature of changes due to digitization specific to the public sector.

Practical implications
The knowledge produced by current and future research in this area is directly applicable for change management. To react productively on the digitization imperative, public managers need to deepen their knowledge of the organizational dimension of digitization.

Originality/value
The paper proposes an agenda for future research, which has the potential to produce both systematic and useful knowledge of how digitization changes central aspects of public sector organizations.
Negative‐pressure closure was superior to tie‐over technique for stabilization of split‐thickness skin graft in large or muscle‐exposing defects: A retrospective study
Authors: Nakamura Yoshiyuki , Fujisawa Yasuhiro , Ishitsuka Yosuke , Tanaka Ryota , Maruyama Hiroshi , Okiyama Naoko , Watanabe Rei , Fujimoto Manabu 
Published: July 2018

AbstractSkin grafts are frequently used for the reconstruction of skin defects, and optimal stabilization of the graft is essential for successful reconstruction. Although the tie‐over technique has been widely used as a standard method in Japan, we sometimes encounter cases with significant graft loss due to suboptimal stabilization of the graft. Reported risk factors for increased graft loss include the following: defects of a large size, with muscle exposure, and located in the trunk and extremities. Recent studies have demonstrated the usefulness of negative‐pressure closure (NPC) for the stabilization of skin grafts due to the uniform pressure it provides across the graft. Therefore, since March 2017, we have used NPC for skin graft stabilization in patients with defects in the trunk and extremities of more than 10 cm in size or with muscle exposure. We carried out a retrospective comparative study of the outcome of the conventional tie‐over technique versus NPC. Mann–Whitney U‐test revealed that NPC showed significantly higher graft survival rate than tie‐over method (P = 0.0012). In addition, NPC showed a tendency toward shorter operative times (from skin graft harvest to the completion of the graft stabilization) than the tie‐over method (P = 0.0931). These results suggest that NPC may be superior to the tie‐over method for stabilization of skin grafts especially in large or muscle‐exposing defects in the trunk or extremities.
Lions and leopards coexist without spatial, temporal or demographic effects of interspecific competition
Authors: Miller Jennifer R. B. , Pitman Ross T. , Mann Gareth K. H. , Fuller Angela K. , Balme Guy A. 
Published: July 2018

Abstract

Although interspecific competition plays a principal role in shaping species behaviour and demography, little is known about the population‐level outcomes of competition between large carnivores, and the mechanisms that facilitate coexistence.

We conducted a multilandscape analysis of two widely distributed, threatened large carnivore competitors to offer insight into coexistence strategies and assist with species‐level conservation.

We evaluated how interference competition affects occupancy, temporal activity and population density of a dominant competitor, the lion (Panthera leo), and its subordinate competitor, the leopard (Panthera pardus). We collected camera‐trap data over 3 years in 10 study sites covering 5,070 km2. We used multispecies occupancy modelling to assess spatial responses in varying environmental and prey conditions and competitor presence, and examined temporal overlap and the relationship between lion and leopard densities across sites and years.

Results showed that both lion and leopard occupancy was independent of—rather than conditional on—their competitor's presence across all environmental covariates. Marginal occupancy probability for leopard was higher in areas with more bushy, “hideable” habitat, human (tourist) activity
and topographic ruggedness, whereas lion occupancy decreased with increasing hideable habitat and increased with higher abundance of very large prey. Temporal overlap was high between carnivores, and there was no detectable relationship between species densities.

Lions pose a threat to the survival of individual leopards, but they exerted no tractable influence on leopard spatial or temporal dynamics. Furthermore, lions did not appear to suppress leopard populations, suggesting that intraguild competitors can coexist in the same areas without population decline. Aligned conservation strategies that promote functioning ecosystems, rather than target individual species, are therefore advised to achieve cost‐ and space‐effective conservation.
‘Strangers in their own Country’: Epideictic Rhetoric and Communal Definition in Enoch Powell's ‘Rivers of Blood’ Speech
Authors: Atkins Judi 
Published: July 2018

AbstractThis article treats Enoch Powell's ‘Rivers of Blood’ speech as an example of the epideictic rhetoric of blame and exclusion. Drawing on a framework proposed by Celeste Michelle Condit, the analysis explores the functions of the address for the speaker and for the audience. Of particular concern are Powell's self‐presentation as a statesman and prophet; his account of the impact and consequences of unrestricted immigration; and his portrayal of a community where ordinary, decent English people were being displaced and victimised by Commonwealth immigrants—a process in which he claimed the authorities were complicit. For the audience, the speech gave public expression to their concerns about immigration, though Powell's predictions of a dystopian future also aroused sentiments of anger and foreboding. Despite the controversy that ensued, the impact of ‘Rivers of Blood’ was far‐reaching, and its influence is still apparent in contemporary debates over immigration.