bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sibe: a computation tool to apply protein sequence statistics to folding and design
Authors: Cheung Ngaam J. , Yu Wookyung 
Published: July 2018

ABSTRACTStatistical analysis plays a significant role in both protein sequences and structures, expanding in recent years from the studies of co-evolution guided single-site mutations to protein folding in silico. Here we describe a computational tool, termed Sibe, with a particular focus on protein sequence analysis, folding and design. Since Sibe has various easy-interface modules, expressive architecture and extensible codes, it is powerful in statistically analyzing sequence data and building energetic potentials in boosting both protein folding and design. In this study, Sibe is used to capture positionally conserved couplings between pairwise amino acids and help rational protein design, in which the pairwise couplings are filtered according to the relative entropy computed from the positional conservations and grouped into several ‘blocks’. A human β2-adrenergic receptor (β2AR) was used to demonstrated that those ‘blocks’ could contribute rational design at functional residues. In addition, Sibe provides protein folding modules based on both the positionally conserved couplings and well-established statistical potentials. Sibe provides various easy to use command-line interfaces in C++ and/or Python. Sibe was developed for compatibility with the ‘big data’ era, and it primarily focuses on protein sequence analysis, in silico folding and design, but it is also applicable to extend for other modeling and predictions of experimental measurements.
Measurements of maize root plasticity under water stress in hydroponic chambers
Authors: Jubery Talukder Z. , Liu Sisi , Lubberstedt Thomas , Ganapathysubramanian Baskar , Attinger Daniel 
Published: July 2018

1.AbstractUnder water stress, plants adjust root traits including depth of root system, root diameter, density of root per volume of soil, hydraulic conductance of root. In this experimental study, we present a method to quantify how hydraulic traits of maize roots adapt to drought. The experiments involve a microfluidic flow sensor and a custom-built pressure chamber, made of transparent plastic for visualization purposes. We measured how maize genotypes (PHB47 and PHZ51) grown for a week in deionized (DI) water and one day in hydroponic nutrients solution (called the irrigated condition) respond to one week of water stress. Conditions of water stress (called drought conditions) were created by mixing Polyethylene Glycol with the nutrients solution. Results show that under drought, the roots of both genotypes respond by approximately halving their global hydraulic conductance. This adjustment seems to be achieved mainly by reductions of the total surface area of the roots. Interestingly, the measured hydraulic conductivity of the roots grown under drought was significantly larger. In all, this study sheds light on how plants adapt to water stress in a hydroponic system, by decreasing root area and increasing root permeability.
Depletion of limiting rDNA structural complexes triggers chromosomal instability and replicative aging ofSaccharomyces cerevisiae
Authors: Fine Ryan D. , Maqani Nazif , Li Mingguang , Franck Elizabeth , Smith Jeffrey S. 
Published: July 2018

AbstractSir2 is a highly conserved NAD+-dependent histone deacetylase that functions in heterochromatin formation and promotes replicative lifespan (RLS) in the budding yeast,Saccharomyces cerevisiae. Within the yeast rDNA locus, Sir2 is required for efficient cohesin recruitment and maintaining stability of the tandem array. In addition to the previously reported depletion of Sir2 in replicatively aged cells, we discovered that subunits of the Sir2 containing complexes, SIR and RENT, were depleted. Several other rDNA structural protein complexes also exhibited age-related depletion, most notably the cohesin complex. We hypothesized that mitotic chromosome instability (CIN) due to cohesin depletion could be a driver of replicative aging. ChIP assays of the residual cohesin (Mcd1-13xMyc) in moderately aged cells showed strong depletion from the rDNA and initial redistribution to the point centromeres, which was then lost in older cells. Despite the shift in cohesin distribution, sister chromatid cohesion was partially attenuated in aged cells and the frequency of chromosome loss was increased. This age-induced CIN was exacerbated in strains lacking Sir2 and its paralog, Hst1, but suppressed in strains that stabilize the rDNA array due to deletion ofFOB1or through caloric restriction (CR). Furthermore, ectopic expression ofMCD1from a doxycycline-inducible promoter was sufficient to suppress rDNA instability in aged cells and to extend RLS. Taken together we conclude that age-induced depletion of cohesin and multiple other nucleolar chromatin factors destabilize the rDNA locus, which then results in general CIN and aneuploidy that shortens RLS.
Zelda potentiates transcription factor binding to zygotic enhancers by increasing local chromatin accessibility during earlyDrosophila melanogasterembryogenesis
Authors: Li Xiao-Yong , Eisen Michael B. 
Published: July 2018

AbstractThe maternally deposited transcription factor Zelda binds to and is required for the activation of a large number of genes in earlyDrosophiladevelopment, and has been suggested to act as a pioneer factor. In this study, we investigated the temporal dynamics of Zelda binding along with the maternal patterning factors Dorsal and Caudal during early embryogenesis. We found in regions bound by Zelda and either Dorsal or Caudal, Zelda binding was detected, and reached maximum levels, earlier than Caudal and Dorsal, providing support of its role as a pioneer factor. We found that Dorsal and Caudal binding correlated strongly with Zelda binding at mitotic cycle 12, suggesting that Zelda is important for early binding by these factors and early onset of their target gene expression. At the same time, we show that among Dorsal target enhancers, the dorsal and ventral ectoderm enhancers are much more strongly associated with Zelda than mesoderm enhancers, revealing an additional function of Zelda in coordinating spatial activity of enhancers. We have also investigated the role of Zelda on chromatin structure. We found that in early embryos, before Dorsal and Caudal are bound at significant levels, Zelda binding is associated with histone acetylation and local histone depletion. These chromatin associated changes accompanied with increased local chromatin accessibility were also detected around Zelda peaks in coding sequences that do not appear to play a role in subsequent transcription factor binding. These findings suggest that Zelda binding itself can lead to chromatin structural changes. Finally, we found that Zelda motifs, both bound and unbound, tend to be associated with positioned nucleosomes, which we suggest may be important for the regulatory specificity of enhancers.
polyRAD: Genotype calling with uncertainty from sequencing data in polyploids and diploids
Authors: Clark Lindsay V. , Lipka Alexander E. , Sacks Erik J. 
Published: July 2018

AbstractLow or uneven read depth is a common limitation of genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), resulting in high missing data rates, heterozygotes miscalled as homozygotes, and uncertainty of allele copy number in heterozygous polyploids. Bayesian genotype calling can mitigate these issues, but previously has only been implemented in software that requires a reference genome or uses priors that may be inappropriate for the population. Here we present several novel Bayesian algorithms that estimate genotype posterior probabilities, all of which are implemented in a new R package, polyRAD. Appropriate priors can be specified for mapping populations, populations in Hardy-Weinberg equilibrium, or structured populations, and in each case can be informed by genotypes at linked markers. The polyRAD software imports read depth from several existing pipelines, and outputs continuous or discrete numerical genotypes suitable for analyses such as genome-wide association and genomic prediction.
Food consumption among income classes and its response to changes in income distribution in rural China
Authors: Ren Yanjun , Zhang Yanjie , Loy Jens-Peter , Glauben Thomas 
Published: July 2018

PurposeGiven the fact that the income disparity has become extremely severe in rural China, the purpose of this paper is to examine heterogeneity in food consumption among various income classes and to investigate the impact of changes in income distribution patterns on food demand in rural China.Design/methodology/approachIn this study, the authors partition the households into five income classes according to the distribution of household per capita net income. Using household data drawn from the China Health and Nutrition Survey in 2011, a two-stage demand model is applied to estimate a food demand system for each of the income classes. After obtaining the estimated income elasticities of eight studied food groups for each income class, the authors then examine the responsiveness of food demand to the changes in income distribution by means of four scenarios with varying income distribution.FindingsThe empirical results indicate that substantial differences in food consumption exist across various income classes. Specifically, the lowest-income households are more sensitive to price and income changes for most studied food groups than the highest-income households are. In general, income responsiveness is higher for meats, aquatic products and dairy products. Based on estimated income elasticities, the projected food consumption under different income distribution patterns shows that changes in income distribution have significant influences on food consumption. In addition, the authors conclude that a more equal distribution of income would be associated with a higher demand for food in rural China.Originality/valueThis paper employs a two-stage demand model to estimate food demand in rural China by income classes. The results imply substantial differences in food demand for various income classes. Therefore, income distribution should be taken into account instead of an average estimation for the population as a whole when investigating food demand in rural China. Given the significant changes in income distribution in rural China, this study provides several important policy implications to alleviate income inequality and poverty, as well as to improve nutrition for lower-income classes.
Examining the inter-relationship among competitive market environments, green supply chain practices, and firm performance
Authors: Choi Seok-Beom , Min Hokey , Joo Hye-Young 
Published: July 2018

PurposeThe purpose of this paper is to assess the impact of competitive market environments on the firm’s decision to adopt green supply chain management (GSCM) practices, while checking to see if the firm’s commitment to particular types of GSCM practices improves its performance.Design/methodology/approachTo confirm a positive link between the firm’s GSCM practices to its performance, the authors collected the data from 322 Korean firms via questionnaire surveys and then analyzed these data using the structural equation model.FindingsAmong various types of GSCM practices, green purchasing has the greatest impact on both manufacturing and marketing performances. Also, internal environmental management positively influenced both manufacturing and marketing performances, whereas cooperation with customers and reverse logistics had no significant impact on the firm’s manufacturing and marketing performances.Originality/valueTo provide a practical advice for firms which are hesitant to embrace green supply chain practices due to skeptical views about their true managerial benefits, this paper discerned more effective GSCM practices from less effective GSCM practices. In so doing, this paper is one of the few studies which pinpointed what types of specific GSCM practices are most effective in enhancing firm performance.
The inverted U-shaped relationship between the network profile and the competitive advantage of supply chains
Authors: Swierczek Artur 
Published: July 2018

PurposeThe purpose of this paper is twofold. First, the author aims to explore if there is a curvilinear relationship between the network rent, generated as a combination of the relational performance of two dyads and the network profile of the triadic supply chains. Second, the author seek to recognize the ideal network profile, consisting of the properties at the node and relationship level, that provides the highest network rents, and thus enables to increase the competitive advantage of supply chains.Design/methodology/approachThe paper opted for an exploratory study using a survey of triads forming supply chains. In order to reveal the capability of yielding the network rent in the examined triads, multiple regression analysis with interaction effects was employed. Having confirmed the existence of supernormal profit, the author investigated the relationship between the network rent and the network index. Finally, a cluster analysis was conducted to compare the network profile in the group of triads generating higher network rents with the cluster yielding relatively lower network rents.FindingsThe obtained findings show that a combination of the relational performance of two dyads contributes to generating the network rent, and thus ensures a more favorable competitive position of supply chains. The results of the study also indicate that there is a significant curvilinear, inverted U-shaped relationship between the network profile and the competitive advantage of triadic supply chains. In addition, the following network properties appear to be particularly important for yielding higher network rents: network centrality, betweenness, network density and network size.Originality/valueThe study contributes to the theory by testing if the network rent can be yielded as a combination of the relational performance of two dyads in the triadic supply chains. The research also indicates that there is a curvilinear relationship between the network rent and the network profile of examined supply chains. Moreover, the study also addresses the link between the network profile, consisting of the multiple network properties simultaneously, in relation to the competitive advantage of supply chains.
An evaluation of supply chain integration across multi-tier supply chains of manufacturing-based SMEs in Malawi
Authors: Kanyoma Kizito Elijah , Agbola Frank Wogbe , Oloruntoba Richard 
Published: July 2018

Purpose
The purpose of this paper is to explain the interrelationships in internal and external supply chain integration (SCI) across multiple tiers of manufacturing-based small and medium-sized enterprises (SMEs) in a developing country, Malawi.

Design/methodology/approach
Utilizing the resource-based view, resource-dependence and network theory perspectives, and drawing on a multiple embedded case-study approach, the research investigated the internal and external linkages within three-tier supplier, manufacturer and retailer SCs and described varying perspectives of SCI across supply chain positions.

Findings
Firms with strategic intra-firm resources were less committed to external integration, deploying their resources as a source of power to dominate and exploit their dependent partners. The SCI across multiple tiers was impaired by dependence but enhanced by interdependence strategies of firms. Although lack of trust, promotion of non-overlapping self-interests, corruption in sourcing processes and resource constraints negatively affected SCI, firm commitment to external integration promoted greater commitment among firms, thus having a positive effect on SCI.

Research limitations/implications
Further analysis of SCI of SME triads and a more systematic longitudinal analysis across other market segments should be explored to generalize the conclusions of this study.

Practical implications
The external influences on dyadic relationships go beyond the interactions of heterogeneous firms in the network to encompass interpersonal interactions across the network, where individuals may potentially prioritize personal connections and sabotage the interests of their firms.

Originality/value
The research explored the internal and external dimensions of SCI in multi-tier SCs of SMEs, and provided for the first time new evidence to show that firm commitment to engaging with partners complements the mechanisms of SCI within a developing country context. It highlights the need to develop trust, eliminate corruption, promote greater commitment of SC partners and encourage greater investment in firms’ resource capabilities to enhance SCI among SMEs.
Sub-administration: ideologies, myths and metaphors
Authors: Farmer David John 
Published: July 2018

Purpose
The purpose of this paper is to recommend that public administration (PA) theory and practice should become more sensitive to its sub-administration, and to suggest how this can be done.

Design/methodology/approach
This conceptual paper maintains that this sub-administration includes those ideologies, myths and metaphors that contribute like an unconscious in shaping (and misshaping) governmental policy and administration. Descriptions of the nature of ideologies, myths and metaphors are given, along with some examples of those that are harmful – such as the ideologies of the American Business Model and neo-liberalism.

Findings
PA should seek to engage and oppose such ideologies, myths and metaphors that are problematic – both those constructed within and without of PA itself. It is recommended that, for such analytical purposes, PA should turn toward post-traditional PA, including the insights of post-modernism and epistemic pluralism.

Originality/value
The concept of sub-administration is of significant utility both for PA theorists and practitioners in strengthening public administrative performance. The author has offered such and/or similar recommendations in earlier publications, including in the International Journal of Organization Theory and Behavior, 19 (1), 90-102: 2016.
Neutrality as it never was: a short treatise on public administration theory
Authors: Miller Hugh T. 
Published: July 2018

PurposeIs public administration neutral? Scholarship does not interpret public administration as neutral, even though, on moral–ethical grounds, it frequently advises neutrality for practitioners. Five main schools of thought are surveyed. Neutrality and alternative expressions of it, such as nonpartisanship, expertise, impartiality or facilitation, are role prescriptions for practicing public administrators, and are typically offered as appropriate comportments in interacting with citizens and groups. At the same time, public administration is undeniably a political institution having political purposes and constitutive impacts. Indeed, the very existence of the administrative state is politically contestable. The paper aims to discuss these issues.Design/methodology/approachCritical reflection, political philosophy, political theory.FindingsScholars across the various schools of thought in public administration do not presuppose the presence of a neutral public administrator. However, there is sometimes an admonition to practitioners to behave as if they were politically neutral.Practical implicationsAdvising practitioners that their practices are neutral masks the fact that public administration is an inherently political institution.Originality/valueNeutral public administration is revealed as empty cant.
The public pursuit of closure: losses, fictions, and endings
Authors: Patterson Patricia 
Published: July 2018

Purpose
This paper raises the possibility that closure is a myth, both in the sense of a narrative guiding a quest and in the sense of a social fiction. The paper aims to discuss this issue.

Design/methodology/approach
The paper examines parts played by public administration practice in quests with subtexts of death, love, and loss, and suggests that overlapping administrative and narrative fictions have their comforts and uses for grieving persons, for organizations, and for the social order.

Findings
The paper confesses ambivalence about the actual existence of closure in historical rather than fictional time.

Originality/value
Using the metaphor of “closing the books,” the paper situates particular public reckonings with human loss in the context of justice-seeking and other public sector companions of “closure,” but resists the narrative closure of the authoritative answer and the happy ending.
Housing information modelling for BIM-embedded housing refurbishment
Authors: Kim Ki Pyung , Park Kenneth Sungho 
Published: July 2018

Purpose
The purpose of this study is to identify building information modelling (BIM) input data sets within a BIM-embedded housing refurbishment process and enable construction professionals to use BIM as an information management platform for housing refurbishment projects.

Design/methodology/approach
A hypothetical case study using BIM tools for a housing refurbishment project is adopted to identify BIM input data sets to create a housing information model within a BIM system. Reliability of the research outcome is examined by conducting a comparative analysis between existing and simulated research outcomes.

Findings
This research identifies essential BIM input data sets during the early design phase. The importance of a well-integrated housing information model containing accurate as-built condition, cost and thermal performance information is essential to use BIM for housing refurbishment. BIM can be feasible for housing refurbishment when an information-enriched housing information model is constructed. Furthermore, the capability of BIM that can enable key project stakeholders to determine the most affordable refurbishment solution among various alternatives is identified as BIM can provide reliable cost estimations and thermal performance of refurbishment alternatives at the early design stage.

Research limitations/implications
The examined refurbishment processes and input data sets are confined to the early design phases as BIM use for housing refurbishment is limited.

Practical implications
This research will contribute to use BIM for housing refurbishment by providing essential BIM input data sets and BIM-embedded refurbishment processes.

Originality/value
This research reveals primary housing information data sets and BIM-embedded refurbishment processes at the early design phase.