bluuebunny/crossref_metadata_2025_split huggingface dataset:
More Insights into the Relation between DNA Ionization Potentials, Single Base Substitutions and Pathogenic Mutations
Authors: Pucci Fabrizio , Rooman Marianne 
Published: October 2018

AbstractIt is nowadays clear that the single base substitutions that occur in the human genome, of which some lead to pathogenic conditions, are non-random and influenced by their flanking nucleobase sequences. However, despite recent progress, the understanding of these “non-local” effects is still far from being achieved. In order to advance this problem, we analyzed the relationship between the base mutability in gene regions and the electron hole transport along the DNA base stacks, as it is one of the mechanisms that have been suggested to contribute to these effects. More precisely, we studied the connection between the observed frequency of single base substitutions and the vertical ionization potential of the base and its flanking sequence, estimated using MP2/6-31G*ab initioquantum chemistry calculations. We found a good correlation between the two quantities, whose sign depend on whether SBS is in an exon, an intron or an untranslated region. Interestingly, the correlation appears to be higher for synonymous than for missense mutations, and when considering the flanking sequence of the substituted base in the 3’ rather than in the 5’ direction. A weaker but still statistically significant correlation it found between the ionization potentials and the pathogenicity of the base substitutions. Moreover, pathogenicity is also preferentially associated with larger changes in ionization potentials upon base substitution. With this analysis we gained new insights into the complex biophysical mechanisms that are at the basis of mutagenesis and pathogenicity, and supported the role of electron-hole transport in these matters.
Epigenetic transmission of cardiometabolic risk in offspring discordant for maternal gestational metabolic fitness
Authors: Guénard Frédéric , Marceau Simon , Simard Serge , Kral John G , Vohl Marie-Claude , Marceau Picard 
Published: October 2018

AbstractOBJECTIVEDiabesity during gestation predisposes offspring to lifetime cardiometabolic risk. We demonstrated that maternal biliopancreatic diversion surgery (BPD) improved metabolic fitness and pregnancies reducing cardiometabolic risk in siblings born after (AMS) compared to before maternal surgery (BMS). We found differential methylation of inflammatory and glucoregulatory genes in peripheral blood cell DNA in offspring and in mothers after BPD compared to preoperative “control” women. Here we study offspring trajectories of cardiometabolic risk markers and determine persistence of the methylome related to body weight (BMI) and gestational weight gain (GWG).RESEARCH DESIGN AND METHODSProspective, cross-sectional study of 133 mothers with 89 BMS and 183 AMS offspring born mean 4 years after BPD and 83 unoperated control women was conducted, and differential methylation patterns in mothers were compared with those of offspring during 2-26 years.RESULTSIndependent of maternal or offspring BMI and GWG, postoperative maternal metabolic fitness was associated with improved cardiometabolic phenotype in AMS vs. BMS offspring sustained beyond puberty. BMS offspring exhibited increasing linear trajectories of weight, cardiometabolic and inflammation risk factorsversusnormative horizontal trajectories of AMS offspring. Methylation differences between AMS and BMS offspring identified 45 625 differentially methylated sites, 73% overlapping with those of mothers vs. controls; 4 446 demonstrated similar sustained directionality of differences in methylation levels; 154 sites exhibited significant correlation coefficients (r≥0.4) overrepresented within genes associated with cardiometabolic risk, growth and inflammation.CONCLUSIONMaternal BPD appears to epigenetically prevent transmission of cardiometabolic risk independent of BMI.
Telomere DNA G-quadruplex folding within actively extending human telomerase
Authors: Jansson Linnea I. , Parks Joseph W. , Hentschel Jendrik , Chang Terren R. , Baral Rishika , Bagshaw Clive R. , Stone Michael D. 
Published: October 2018

ABSTRACTTelomerase maintains telomere length by reverse transcribing short G-rich DNA repeat sequences from its internal RNA template. G-rich telomere DNA repeats readily fold into G-quadruplex (GQ) structures in vitro, and the presence of GQ-prone sequences throughout the genome introduces challenges to replication in vivo. Using a combination of ensemble and single-molecule telomerase assays we discovered that GQ folding of the nascent DNA product during processive addition of multiple telomere repeats modulates the kinetics of telomerase catalysis and dissociation. Telomerase reactions performed with telomere DNA primers of varying sequence or using K+ versus Li+ salts yield changes in DNA product profiles consistent with formation of GQ structure within the telomerase-DNA complex. Single-molecule FRET experiments reveal complex DNA structural dynamics during real-time catalysis, supporting the notion of nascent product folding within the active telomerase complex. To explain the observed distributions of telomere products, we fit telomerase time series data to a global kinetic model that converges to a unique set of rate constants describing each successive telomere repeat addition cycle. Our results highlight the potential influence of the intrinsic folding properties of telomere DNA during telomerase catalysis and provide a detailed characterization of GQ modulation of polymerase function.SIGNIFICANCETelomeres protect the ends of linear chromosomes from illicit DNA processing events that can threaten genome stability. Telomere structure is built upon repetitive G-rich DNA repeat sequences that have the ability to fold into stable secondary structures called G-quadruplexes (GQs). In rapidly dividing cells, including the majority of human cancers, telomeres are maintained by the specialized telomerase enzyme. Thus, telomerase and its telomere DNA substrates represent important targets for developing novel cancer drugs. In this work, we provide evidence for GQ folding within the newly synthesized DNA product of an actively extending telomerase enzyme. Our results highlight the delicate interplay between the structural properties of telomere DNA and telomerase function.
Blind lattice-parameter determination of cubic and tetragonal phases with high accuracy using a single EBSD pattern
Authors: Han Ming , Chen Chen , Zhao Guangming , Li Lili , Nolze Gert , Yu Baojun , Huang Xiaodong , Zhu Ye 
Published: October 2018

The Bravais lattices and their lattice parameters are blindly determined using electron backscatter diffraction (EBSD) patterns of materials with cubic or tetragonal crystal structures. Since the geometric relationships in a single EBSD pattern are overdetermined, the relative errors of determining the lattice parameters as well as the axial ratios are confined to about 0.7 ± 0.4% and 0.07 ± 0.03%, respectively, for ideal simulated EBSD patterns. The accuracy of the crystal orientation determination reaches about 0.06 ± 0.03°. With careful manual band detection, the accuracy of determining lattice parameters from experimental patterns can be as good as from simulated patterns, although the results from simulated patterns are often better than expermental patterns, which are lower quality and contain uncertain systematic errors. The reasonably high accuracy is obtained primarily because the detection of the diffracting-plane traces and zone axes is relatively accurate. The results here demonstrate that the developed procedure based on the EBSD technique presents a reliable tool for crystallographic characterization of the Bravais lattices of unknown phases.
Solving a mixture model of two-phase flow with velocity non-equilibrium using WENO wavelet methods
Authors: Kozakevicius Alice de Jesus , Zeidan Dia , Schmidt Alex A. , Jakobsson Stefan 
Published: October 2018

Purpose
The purpose of this work is to present the implementation of weighted essentially non-oscillatory (WENO) wavelet methods for solving multiphase flow problems. The particular interest is gas–liquid two-phase mixture with velocity non-equilibrium. Numerical simulations are carried out on different scenarios of one-dimensional Riemann problems for gas–liquid flows. Results are validated and qualitatively compared with solutions provided by other standard numerical methods.

Design/methodology/approach
This paper extends the framework of WENO wavelet adaptive method to a fully hyperbolic two-phase flow model in a conservative form. The grid adaptivity in each time step is provided by the application of a thresholded interpolating wavelet transform. This facilitates the construction of a small yet effective sparse point representation of the solution. The method of Lax–Friedrich flux splitting is used to resolve the spatial operator in which the flux derivatives are approximated by the WENO scheme.

Findings
Hyperbolic models of two-phase flow in conservative form are efficiently solved, as shocks and rarefaction waves are precisely captured by the chosen methodology. Substantial computational gains are obtained through the grid reduction feature while maintaining the quality of the solutions. The results indicate that WENO wavelet methods are robust and sufficient to accurately simulate gas–liquid mixtures.

Originality/value
Resolution of two-phase flows is rarely studied using WENO wavelet methods. It is the first time such a study on the relative velocity is reported in two-phase flows using such methods.
Influence of factors on collapse risk of loess tunnel: a multi-index assessment model
Authors: Zhang Xueliang , Wang Meixia , Zhou Binghua , Wang Xintong 
Published: October 2018

Purpose
Because of the properties of loess, the occurrence of collapse following deformation of a large settlement is a common problem during the excavation of tunnels on loess ground. Hence, risk management for safer loess tunnel construction is of great significance. The purpose of this paper is to explore the influence of factors on collapse risk of loess tunnels and establish a risk assessment model using rough set theory and extension theory.

Design/methodology/approach
The surrounding rock level, groundwater conditions, burial depth, excavation method and support close time were selected as the factors and settlement deformation was the verification index for risk assessment. First, using rough set theory, the influence of risk factors on the collapse risk of loess tunnels was calculated by researching engineering data of excavated sections. Then, a collapse risk assessment model was developed based on extension theory. As the final step, the model was applied to practical engineering in the Loess Plateau of China.

Findings
The weights of surrounding rock level, groundwater conditions, burial depth, excavation method and support close time obtained using rough set theory were respectively 10.811 per cent, 18.919 per cent, 24.324 per cent, 40.541 per cent and 5.406 per cent. The assessment results obtained using the model were in good agreement with field observations.

Originality/value
This study highlights key points in collapse risk management of loess tunnels, which could be very useful for future construction methods. The model, using easily obtained parameters, helps in predicting the collapse risk level of loess tunnels excavated under different geological conditions and by different construction organizations and provides a reference for future studies.
Factors confronting quantity surveying practice: the case of Nigeria
Authors: Ogunsina Olusola , Ekwus Obiegbu Micah , Adeniyi Onaopepo 
Published: October 2018

Purpose
As the challenges confronting a system are better addressed when known and understood, this paper aims to report the findings of a study that investigated the factors confronting professional quantity surveying using Nigeria as a case.

Design/methodology/approach
A questionnaire was developed and pre-tested as the instrument for collecting data. A total of 64 quantity surveyors practicing in Lagos, Port Harcourt and Enugu completed the questionnaire out of a non-probabilistic sample of 100. Severity Index and Spearman rank correlation coefficient were used in data analysis.

Findings
The outcome revealed that the top five factors perceived to be confronting the profession include poor marketing of the profession, opposition from engineers, the dominance of multinational companies that do not have quantity surveying as a distinct profession in their country of origin, widespread corruption in Nigeria and professional incompetence of some quantity surveyors. Furthermore, the two categories of respondents – professional quantity surveyors and probationers – agree in their ranking of the factors confronting the profession. The ranking of the 17 factors between the two categories of respondents was tested using Spearman’s rho. The result showed that the difference in perception of professional members of the Nigerian Institute of Quantity Surveyors and the probationers with regard to factors confronting the quantity surveying profession is not significant at p < 0.01. These findings are then discussed in the light of previous works, and implications for both academics and professionals within the quantity surveying profession were highlighted.

Originality/value
This study has highlighted the key issues to consider as stakeholders attempt to advance the course of quantity surveying and construction cost management profession.
Coworking spaces: a new way of achieving productivity
Authors: Bueno Salvador , Rodríguez-Baltanás Gonzalo , Gallego M. Dolores 
Published: October 2018

Purpose
This paper aims to explore the relationship between coworking spaces and productivity.

Design/methodology/approach
A research model was designed to carry out the analysis. Specifically, this model attempts to reveal the influence of social interactions and the coworking environment on productivity. Furthermore, three moderated variables were incorporated into the model: gender, age and level of education. A Web-based survey was conducted.

Findings
The findings confirm the positive influence of social interactions and coworking environment on productivity.

Research limitations/implications
There are two limitations. First, it is based on the perception of coworkers. It would be interesting to add the perception of coworking space managers to provide more solid findings. The second limitation is that it has not suggested any additional potential factors which could affect productivity.

Practical implications
Implications of this study are grouped into two categories. First, from an academic perspective, it contributes to the development of knowledge about the increasing use of coworking spaces. Second, from a managerial perspective, this paper highlights how environmental factors and the facilities of a workplace can help to achieve better conditions for productivity, in particular in coworking spaces.

Social implications
Furthermore, the use of social interactions in professional relationships can be understood as an alternative way to carry out new ways of doing business.

Originality/value
This paper contributes to the enrichment of knowledge-concerning coworking spaces developed a pioneering study.
Organizational archives and historical narratives
Authors: Barros Amon , Carneiro Adéle de Toledo , Wanderley Sergio 
Published: October 2018

PurposeThe purpose of this paper is to present the role of reflexivity in relation to archives and narratives.Design/methodology/approachThe authors problematize the concept of “archive,” by engaging with debates in philosophy and the archival theory. The authors also revisit historical theories and debates on the role of the narrative within historiography. Finally, the authors consider reflexivity as a methodological attitude taken by the researcher at all stages of the investigation from challenging theoretical assumptions of empirical materials to questioning the very narrative that is created when looking for alternative ones.FindingsThis paper poses questions about documents and archives that emerge from reflexivity. The authors claim that reflexivity is an ethos that allows researchers to keep the multiple narratives in which they are entangled in check. The paper brings a framework that allows researchers to use reflexivity to become more conscious of the complexities and ambiguities within the research process that leads to the writing of historical narratives.Research limitations/implicationsThis paper points to the need to enhance the reflexivity at every stage of the research, including “interrogating” the archives and documents, which are compiled under a narrative.Practical implicationsThe authors highlighted the multiple characteristics of archives, their meanings and the possibilities of writing narratives about them through reflexivity. The authors have the historical narrative as one possible reconstruction of a historical object, which is connected to the production conditions of the text. Through reflexivity, the authors discussed the socially constructed nature of the documents and the archives. Finally, the authors believe that debates around the production of this knowledge should continue, focusing especially on building bridges with the field of history.Social implicationsHistorical narratives do not depend on the scientific character of historical sources, but it considers reflexivity by the researcher regarding the search, collection, reading and analysis of historical documents. In addition, it is necessary to think about the use of documents and archives and histories in a reflective way for a writing of history and, indirectly, for a contextual understanding of the time observed and as forged sources – or discarded – and made available.Originality/valueChallenging the use of documents and archives in a reflexive way for the writing of historical narratives and for contextual understanding of the past is key to a richer relationship between management and history. This paper points to the role of reflexivity in relation to archives and narratives in the practice of (re)constructing the organizational past from memories and silences. It also highlights how reflexivity can be incorporated in the research process to enrich the writing of the historical narrative.
Design optimisation for cold-formed steel residential roof truss using genetic algorithm
Authors: Kok Ka Yee , Lau Hieng Ho , Phan Thanh Duoc , Ting TIina Chui Huon 
Published: October 2018

Purpose
This paper aims to present the design optimisation using genetic algorithm (GA) to achieve the highest strength to weight (S/W) ratio, for cold-formed steel residential roof truss.

Design/methodology/approach
The GA developed in this research simultaneously optimises roof pitch, truss configurations, joint coordinates and applied loading of typical dual-pitched symmetrical residential roof truss. The residential roof truss was considered with incremental uniform distributed loading, in both gravitational and uplift directions. The structural analyses of trusses were executed in this GA using finite element toolbox. The ultimate strength and serviceability of trusses were checked through the design formulation implemented in GA, according to the Australian standard, AS/NZS 4600 Cold-formed Steel Structures.

Findings
An optimum double-Fink roof truss which possess highest S/W ratio using GA was determined, with optimum roof pitch of 15Â°. The optimised roof truss is suitable for industrial application with its higher S/W ratio and cost-effectiveness. The combined methodology of multi-level optimisation and simultaneous optimisation developed in this research could determine optimum roof truss with consistent S/W ratio, although with huge GA search space.

Research limitations/implications
The sizing of roof truss member is not optimised in this paper. Only single type of cold-formed steel section is used throughout the whole optimisation. The design of truss connection is not considered in this paper. The corresponding connection costs are not included in the proposed optimisation.

Practical implications
The optimum roof truss presented in this paper is suitable for industrial application with higher S/W ratio and lower cost, in either gravitational or uplift loading configurations.

Originality/value
This research demonstrates the approaches in combining multi-level optimisation and simultaneous optimisation to handle large number of variables and hence executed an efficient design optimisation. The GA designed in this research determines the optimum residential roof truss with highest S/W ratio, instead of lightest truss weight in previous studies.
Guidelines for the Design, Installation, Operation and Maintenance of Safety Relief Devices for Steam Surface Condensers
Authors: Nightingale Darren M. 
Published: October 2018

Steam surface condensers may require several different relief devices for safe operation. Atmospheric relief devices are typically utilized for the safe relief of over-pressure on the shell-side (LP steam). This is to protect and prevent steam surface condensers, often including steam turbine exhaust hoods, from exceeding specified design pressures. In addition to shell-side safety devices, relief devices for the tube-side (cooling water), such as water box pressure & vacuum relief, venting and air removal valves, all perform a similar function.
This paper provides a thorough background to all the types of condenser safety relief devices currently available. The latest applicable standards, codes and guidelines for these safety relief devices are reviewed, in conjunction with the current methodology for the correct design and sizing of such devices. Several sample calculations and working examples for the correct sizing of safety devices are provided for reference. The paper includes a review of the relative attributes and considerations for the appropriate selection of each of these types of safety devices, e.g. rupture discs versus atmospheric relief valves for shell-side protection. The paper concludes with a comprehensive review of the latest guidelines for the installation, operation, and maintenance for these safety devices, including guidance on other aspects such as preferred locations, exhaust & vent piping, routine inspection, and testing requirements.