bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extraction of a recombinant full-length NADPH-cytochrome P450 oxidoreductase from bacterial membranes: effect of detergents and additives
Authors: Arafeh Sara A. , Galiakhmetov Azamat R. , Kovrigina Elizaveta A. , Fellin Eric , Kovrigin Evgenii L. 
Published: March 2018

ABSTRACTNADPH-cytochrome P450 oxidoreductase (POR) is a membrane protein in the endoplasmic reticulum of eukaryotic cells. POR is as a key reducing partner for a number of cytochrome P450 proteins involved in different metabolic degradation and signaling pathways. Preparation of the full-length recombinant POR expressed in bacteria has been reported and, typically, involved the use of Triton X-100 detergent for extraction of the overexpressed POR from bacterial membranes. However, extraction efficiency is always relatively low hindering structural studies, particularly—the NMR spectroscopy requiring isotopic enrichment. In this paper, we assessed the effect of a variety of detergents and additives on the efficiency of the membrane-extraction step in POR preparation protocol. We evaluated non-ionic detergents with the variable hydrophobicity (Triton X-100, X-114, and X-405) and structure (Triton X-100, TWEEN-20, Brij-35), a zwitterionic/non-ionic detergent combination (Triton X-100 and CHAPS), as well as a range of alkylamines and polyamines as additives to the conventional extraction buffer containing Triton X-100. None of the detergents or detergent-additive combinations yielded better extraction efficiency than the conventional protocol with the Triton X-100. Lack of variation of the extraction yield allows to hypothesize that the conventional protocol extracts all of the available natively-folded monomeric POR while the remaining fraction is possibly an unfolded aggregated POR, which did not insert in the membranes during expression. We propose that the yield of soluble POR may be increased by a careful optimization of expression conditions while monitoring the distribution of POR between soluble and insoluble fractions in the detergent extraction step.
Multi-study inference of regulatory networks for more accurate models of gene regulation
Authors: Castro Dayanne M. , de Veaux Nicholas R. , Miraldi Emily R. , Bonneau Richard 
Published: March 2018

AbstractGene regulatory networks are composed of sub-networks that are often shared across biological processes, cell-types, and organisms. Leveraging multiple sources of information, such as publicly available gene expression datasets, could therefore be helpful when learning a network of interest. Integrating data across different studies, however, raises numerous technical concerns. Hence, a common approach in network inference, and broadly in genomics research, is to separately learn models from each dataset and combine the results. Individual models, however, often suffer from under-sampling, poor generalization and limited network recovery. In this study, we explore previous integration strategies, such as batch-correction and model ensembles, and introduce a new multitask learning approach for joint network inference across several datasets. Our method initially estimates the activities of transcription factors, and subsequently, infers the relevant network topology. As regulatory interactions are context-dependent, we estimate model coefficients as a combination of both dataset-specific and conserved components. In addition, adaptive penalties may be used to favor models that include interactions derived from multiple sources of prior knowledge including orthogonal genomics experiments. We evaluate generalization and network recovery using examples fromBacillus subtilisandSaccharomyces cerevisiae, and show that sharing information across models improves network reconstruction. Finally, we demonstrate robustness to both false positives in the prior information and heterogeneity among datasets.
Coordinate transformation uncertainty analysis and reduction using hybrid reference system for aircraft assembly
Authors: Deng Zhengping , Li Shuanggao , Huang Xiang 
Published: March 2018

Purpose
In aircraft assembly, standard reference points with nominal coordinates are commonly applied for coordinate transformation between multiple measurement stations and the assembly coordinate system. For several reasons in practical application, these points often fail to envelop the key assembly space, which leads to large transformation uncertainty. This paper aims to analyze and further reduce the coordinate transformation uncertainty by introducing a new hybrid reference system (HRS).

Design/methodology/approach
Several temporary extension points without known coordinates are added to enhance the tightness between different stations, especially at the weakness area in the network, thus constituting an HRS together with the existing standard reference points. The coordinate transformation model of the HRS-based measurement network is established based on an extend Gauss–Markov model. By using the geometrical differential property and variance-covariance propagation law, the covariance matrixes in the transformation model are calculated, and the analytical solution of the uncertainties of transformation parameters are ultimately derived. The transformation uncertainty of each check points is presented by Helmert error expression.

Findings
The proposed analytical solution of transformation uncertainty is verified using the state-of-the-art Monte Carlo simulation method, but the solution process is simpler and the computation expenses are much less.

Practical implications
The HRS with three temporary extension points is practically applied to a tail boom in-site measurement for assembly. The average transformation uncertainty has been reduced by 26 per cent to less than 0.05 mm.

Originality/value
The hybrid coordinate transformation model is proposed for the first time. The HRS method for transformation uncertainty reduction is more economical and practical than increasing the number of standard reference points.
Gender differences in growth of Spanish university spin-offs
Authors: Rodríguez-Gulías María Jesús , Fernández-López Sara , Rodeiro-Pazos David 
Published: March 2018

PurposeThe purpose of this paper is to explore the hypothesis that the female-owned university spin-off organizations (USOs) have a similar resource endowment and, as a consequence, growth rates similar to the male-owned USOs.Design/methodology/approachA unique and original longitudinal data set, which is an unbalanced panel, consisting of 120 Spanish USOs over the period 2001-2010 has been constructed. The methodology includes the analysis of mean differences (t-test) and dynamic panel data models.FindingsThe results confirmed that there are no gender differences in either the firms’ initial resource endowment or in the preference for industries. There is no gender effect on the USOs’ growth, but the initial endowment resources matter. Thus the financial, human and technological resources have a positive effect on the USOs’ growth. This evidence suggests that the USOs’ context may mitigate the initial resource endowment of the female-owned firms and their preferences for traditional industries, showing similar rates of growth than male-owned USOs.Research limitations/implicationsOwners’ gender has been used as a proxy for founders’ gender. Also, only USOs included in the SABI database have been considered as part of the sample; the significant number of USOs that did not reveal information about their owners have been discarded.Practical implicationsIt is important to continue supporting academic entrepreneurship, as in the university context, firm growth is not affected by gender differences. However, given that the percentage of female owners in university entrepreneurship is still lower compared to entrepreneurship in general, the universities’ entrepreneur programmes targeting women must adopt a gendered perspective.Originality/valueLiterature on USOs has traditionally analyzed the firm-specific characteristics that impact their growth without considering the influence of the owners’ gender. In this paper, an attempt to fill this gap has been made using a sample of 120 Spanish USOs and by applying the dynamic panel data methodology. In particular, it has been argued that the university context from which USOs emerge allows female-owned USOs to have a similar resource endowment and, as a consequence, a similar growth when compared to male-owned USOs.
An ethnocentric perspective of foreign multi-brand retail in India
Authors: Banerji Diptiman , Mishra Prashant 
Published: March 2018

Purpose
The purpose of this paper is to understand the ethnocentric tendencies of Indian consumers towards foreign multi-brand retailers (FMBRs), and the influence that such ethnocentrism has on their attitudes towards, and future purchasing behaviour from, these international retailers.

Design/methodology/approach
The paper used a mall intercept method with a randomised data collection process to secure data from 119 organised retail shoppers in a major metropolitan Indian city. The analysis was carried out using analysis of covariance, bootstrapping mediation, multiple regression analysis, and Johnson’s relative weight analysis.

Findings
Two main results are as follows: concern for livelihoods of small retailers and a perception that earnings of foreign retailers are unjust are revealed as the most significant drivers of negative attitude towards FMBRs, and although high ethnocentric customers have a strong negative attitude towards FMBRs, they are open to the idea of making future purchases of goods that are not available with small retailers, from the foreign retail outlets.

Research limitations/implications
The study sample is from a single metropolitan city, albeit one which serves as a miniature version of the Indian society. As a limitation, the results might not be generalisable to small, non-metropolitan Indian towns.

Practical implications
These results provide valuable input regarding the marketing strategy and sustainability of foreign retailers planning to launch operations in India. For example, FMBRs should position themselves as not being in competition with existing small retail shops by offering a different array of products. Further, younger and more educated Indians are the least ethnocentric towards FMBRs, thus making them an attractive target segment.

Originality/value
Extant research has studied consumer ethnocentrism of Indian consumers towards foreign brands and products, but not towards FMBRs. This paper attempts to fill that research gap.
The use of social media by South African organisations
Authors: Dlamini Nomusa Nomhle , Johnston Kevin 
Published: March 2018

Purpose
The purpose of this paper is to present how organisations in South Africa are using social media. The paper further explores the value of social media to South African organisations and if it is important for an organisation to have a social media presence.

Design/methodology/approach
The study used quantitative research methods to answer the main research question and sub-questions.

Findings
The data collected revealed that most organisations in South Africa are using social media for free advertising, CRM and marketing. The popular social media sites used by these organisations are Facebook and Twitter, with LinkedIn increasing in popularity. The data further revealed that social media is important in organisations for relationship building, contact keeping advertising, marketing, attracting customers, brand management and information gathering.

Research limitations/implications
The role of social media is changing, it was initially a marketing tool, but the findings revealed that majority of organisations are using social media for free advertising, CRM and marketing. Social media is an easy CRM tool that offers effective and efficient capabilities.

Practical implications
It is important to use integrate social media with the organisations processes to market and advertise new products, it is an instant and cost-saving way of communicating with customers, and helps in reaching and attracting new customers.

Social implications
Social media is important for keeping contact and building relationships with customers, advertising and marketing, way to attract customers, brand management tool and gathering information.

Originality/value
The study provides guidance to how organisation can use social media, identifying the value of using social media and highlighting the importance of social media in an organisation in the South African context.
Corporate financial structure and firm’s decision to export
Authors: Miravitlles Paloma , Mora Toni , Achcaoucaou Fariza 
Published: March 2018

PurposeThe purpose of this paper is to analyse the decision to export in relation to financial issues, specifically the impact of corporate financial structure on a firm’s export propensity (the likelihood of a firm becoming an exporter) by firm size.Design/methodology/approachA multivariate probit model is applied to a sample of 8,019 Spanish manufacturing firms drawn from the Iberian Balance Sheet Analysis System (SABI). The analysis is performed separately for small, medium and large firms.FindingsThe paper evidences, by firm size, a positive link between ownership concentration and export propensity, although for SMEs if shareholder concentration is very high it can be counterproductive. In addition, a high degree of liquidity influences the probability of entering export markets, while those firms that face high costs as result of their export activity may need to become indebted in order to secure the necessary financial resources. However, the strength of these latter effects differs in SMEs.Originality/valueThis paper broadens the understanding of the relationship between firms’ export propensity and their financial health and ownership concentration, an internal factor not previously considered in the international business literature despite its relevance for firm’s decision to export. The paper highlights that their influence is not uniform but affects firms of different sizes in different ways. This is of interest and value to scholars, investors and policy makers worldwide, since handling corporate financial structure and international strategies needs to be addressed in today’s global business environment.
A horizontally gene transferred copper resistance locus confers hyper‐resistance to antibacterial copper toxicity and enables survival of community acquired methicillin resistant Staphylococcus aureus USA300 in macrophages
Authors: Purves Joanne , Thomas Jamie , Riboldi Gustavo P. , Zapotoczna Marta , Tarrant Emma , Andrew Peter W. , Londoño Alejandra , Planet Paul J. , Geoghegan Joan A. , Waldron Kevin J. , Morrissey Julie A. 
Published: March 2018

SummaryExcess copper is highly toxic and forms part of the host innate immune system's antibacterial arsenal, accumulating at sites of infection and acting within macrophages to kill engulfed pathogens. We show for the first time that a novel, horizontally gene transferred copper resistance locus (copXL), uniquely associated with the SCCmec elements of the highly virulent, epidemic, community acquired methicillin resistant Staphylococcus aureus (CA‐MRSA) USA300, confers copper hyper‐resistance. These genes are additional to existing core genome copper resistance mechanisms, and are not found in typical S. aureus lineages, but are increasingly identified in emerging pathogenic isolates. Our data show that CopX, a putative P1B‐3‐ATPase efflux transporter, and CopL, a novel lipoprotein, confer copper hyper‐resistance compared to typical S. aureus strains. The copXL genes form an operon that is tightly repressed in low copper environments by the copper regulator CsoR. Significantly, CopX and CopL are important for S. aureus USA300 intracellular survival within macrophages. Therefore, the emergence of new S. aureus clones with the copXL locus has significant implications for public health because these genes confer increased resistance to antibacterial copper toxicity, enhancing bacterial fitness by altering S. aureus interaction with innate immunity.
Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments
Authors: Scott Kathleen M. , Williams John , Porter Cody M. B. , Russel Sydney , Harmer Tara L. , Paul John H. , Antonen Kirsten M. , Bridges Megan K. , Camper Gary J. , Campla Christie K. , Casella Leila G. , Chase Eva , Conrad James W. , Cruz Mercedez C. , Dunlap Darren S. , Duran Laura , Fahsbender Elizabeth M. , Goldsmith Dawn B. , Keeley Ryan F. , Kondoff Matthew R. , Kussy Breanna I. , Lane Marannda K. , Lawler Stephanie , Leigh Brittany A. , Lewis Courtney , Lostal Lygia M. , Marking Devon , Mancera Paola A. , McClenthan Evan C. , McIntyre Emily A. , Mine Jessica A. , Modi Swapnil , Moore Brittney D. , Morgan William A. , Nelson Kaleigh M. , Nguyen Kimmy N. , Ogburn Nicholas , Parrino David G. , Pedapudi Anangamanjari D. , Pelham Rebecca P. , Preece Amanda M. , Rampersad Elizabeth A. , Richardson Jason C. , Rodgers Christina M. , Schaffer Brent L. , Sheridan Nancy E. , Solone Michael R. , Staley Zachery R. , Tabuchi Maki , Waide Ramond J. , Wanjugi Pauline W. , Young Suzanne , Clum Alicia , Daum Chris , Huntemann Marcel , Ivanova Natalia , Kyrpides Nikos , Mikhailova Natalia , Palaniappan Krishnaveni , Pillay Manoj , Reddy T.B.K. , Shapiro Nicole , Stamatis Dimitrios , Varghese Neha , Woyke Tanja , Boden Rich , Freyermuth Sharyn K. , Kerfeld Cheryl A. 
Published: March 2018

SummaryChemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL‐ and GGDEF‐domain proteins and methyl‐accepting chemotaxis proteins) despite their small sizes (2.1–3.1 Mbp). An array of sulfur‐oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2‐6, acquired via horizontal gene transfer. In addition to high‐affinity cbb3 cytochrome c oxidase, some also encode cytochrome bd‐type quinol oxidase or ba3‐type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.
Identification of inner membrane translocase components of TolC‐mediated secretion in the cyanobacterium Synechocystis sp. PCC 6803
Authors: Gonçalves Cátia F. , Pacheco Catarina C. , Tamagnini Paula , Oliveira Paulo 
Published: March 2018

SummaryCyanobacteria were the first organisms ever to perform oxygenic photosynthesis and still significantly contribute to primary production on a global scale. To assure the proper functioning of their primary metabolism and cell homeostasis, cyanobacteria must rely on efficient transport systems to cross their multilayered cell envelope. However, cyanobacterial secretion mechanisms remain largely unknown. Here, we report on the identification of 11 putative inner membrane translocase components of TolC‐mediated secretion in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Gene‐inactivation of each of the candidate genes followed by a comprehensive phenotypic characterization allowed to link specific protein components to the processes of protein export (as part of the type I secretion system) and drug efflux (part of the resistance‐division‐nodulation efflux pumps). In addition, mutants in genes sll0141, sll0180 and slr0369 exhibited alterations in pilin glycosylation, but pili structures could still be observed by transmission electron microscopy. By studying the release of outer membrane vesicles (OMVs), an alternative secretion route, on mutants with impaired secretory functions we suggest that the hyper‐vesiculating phenotype of the TolC‐deficient mutant is related to cell envelope stress management. Altogether, these findings highlight how both classical (TolC‐mediated) and nonclassical (OMVs‐mediated) secretion systems are crucial for cyanobacterial cell homeostasis.
The three stages of the anti‐incumbency vote: Retrospective economic voting in young and established democracies
Authors: BOCHSLER DANIEL , HÄNNI MIRIAM 
Published: March 2018

AbstractEconomic prosperity is the best recipe for an incumbent government to be re‐elected. However, the financial crisis was significantly more consequential for governing parties in young rather than in established democracies. This article introduces the age of democracy as a contextual explanation which moderates the degree to which citizens vote retrospectively. It shows a curvilinear effect of the age of democracy on retrospective economic voting. In a first stage after the transition to democracy, reform governments suffer from a general anti‐incumbency effect, unrelated to economic performance. In a second step, citizens in young democracies relate the legitimacy of democratic actors to their economic performance rather than to procedural rules, and connect economic outcomes closely to incumbent support. As democracies mature, actors profit from a reservoir of legitimacy, and retrospective voting declines. Empirically, these hypotheses are corroborated by data on vote change and economic performance in 59 democracies worldwide, over 25 years.
Fair treatment, fair play? The relationship between fair treatment perceptions, political trust and compliant and cooperative attitudes cross‐nationally
Authors: MARIEN SOFIE , WERNER HANNAH 
Published: March 2018

AbstractObtaining citizens’ voluntary compliance with political decisions is a fundamental democratic challenge. Fair treatment by public officials plays a key role in theoretical and empirical studies on citizens’ compliance and cooperation. Yet it is unclear whether citizens within different societies react to (un)fair treatment in the same way. Using multilevel structural equation modelling and multilevel regression analysis on the European Social Survey 2010–2 (N = 52,458), this article shows that perceptions of fair treatment by police officers are associated with higher levels of trust in political institutions and in turn stronger compliant and cooperative attitudes of citizens in 27 countries. Yet the link between perceptions of unfair treatment and institutional trust is stronger in countries in which fair behaviour is more prevalent. While fair treatment is often considered to be a universal norm affecting citizens in a uniform way, this article sheds light on important cross‐national variations.