bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposon-insertion sequencing screens unveil requirements for EHEC growth and intestinal colonization
Authors: Warr Alyson R. , Hubbard Troy P. , Munera Diana , Blondel Carlos J. , Abel zur Wiesch Pia , Abel Sören , Wang Xiaoxue , Davis Brigid M , Waldor Matthew K. 
Published: February 2019

AbstractEnterohemorrhagicEscherichia coliO157:H7 (EHEC) is an important food-borne pathogen that colonizes the colon. Transposon-insertion sequencing (TIS) was used to identify genes required for EHEC and commensalE. coliK-12 growth in vitro and for EHEC growth in vivo in the infant rabbit colon. Surprisingly, many conserved loci contribute to EHEC’s but not to K-12’s growth in vitro, suggesting that gene acquisition during EHEC evolution has heightened the pathogen’s reliance on certain metabolic processes that are dispensable for K-12. There was a restrictive bottleneck for EHEC colonization of the rabbit colon, which complicated identification of EHEC genes facilitating growth in vivo. Both a refined version of an existing analytic framework as well as PCA-based analysis were used to compensate for the effects of the infection bottleneck. These analyses confirmed that the EHEC LEE-encoded type III secretion apparatus is required for growth in vivo and revealed that only a few effectors are critical for in vivo fitness. Numerous mutants not previously associated with EHEC survival/growth in vivo also appeared attenuated in vivo, and a subset of these putative in vivo fitness factors were validated. Some were found to contribute to efficient type-three secretion while others, includingtatABC, oxyR, envC, acrAB, andcvpA, promote EHEC resistance to host-derived stresses encountered in vivo.cvpA, which is also required for intestinal growth of several other enteric pathogens, proved to be required for EHEC,Vibrio choleraeandVibrio parahaemolyticusresistance to the bile salt deoxycholate. Collectively, our findings provide a comprehensive framework for understanding EHEC growth in the intestine.Author SummaryEnterohemorrhagicE. coli(EHEC) are important food-borne pathogens that infect the colon. We created a highly saturated EHEC transposon library and used transposon insertion sequencing to identify the genes required for EHEC growth in vitro and in vivo in the infant rabbit colon. We found that there is a large infection bottleneck in the rabbit model of intestinal colonization, and refined two analytic approaches to facilitate rigorous identification of new EHEC genes that promote fitness in vivo. Besides the known type III secretion system, more than 200 additional genes were found to contribute to EHEC survival and/or growth within the intestine. The requirement for some of these new in vivo fitness factors was confirmed, and their contributions to infection were investigated. This set of genes should be of considerable value for future studies elucidating the processes that enable the pathogen to proliferate in vivo and for design of new therapeutics.
Optical properties of living corals determined with diffuse reflectance spectroscopy
Authors: Jacques Steven L. , Wangpraseurt Daniel , Kühl Michael 
Published: February 2019

AbstractThe internal light field and thus light exposure of the photosymbiotic microalgae (Symbiodinium sp.) in corals is strongly modulated by the optical properties of coral tissue and skeleton. While there are numerous studies documenting the light microenvironment in corals, there are only few measurements of the inherent optical properties of corals in the literature, and this has hampered a more quantitative understanding of coral optics. Here we present a study of the optical properties of 26 live coral samples, representative of 11 coral species and spanning a variety of morphotypes. We employed well-established fiber-optic reflectance spectroscopy techniques from biomedical optics using two methods: (1) A source and a detection fiber separated by a variable distance measured the lateral spread of light in corals, dominated by the skeleton; (2) A fiber-optic field radiance probe measured the diffuse reflectance from the coral surface, dominated by the living coral tissue. Analysis based on diffusion theory and Monte Carlo simulation yielded estimates of the bulk scattering and absorption coefficients of the coral tissue and skeleton, in the 750-1030 nm wavelength range. Extrapolating into the spectral region of photosynthetically active radiation (PAR, 400-700 nm) allowed estimation of the optical depth of absorption by the main Symbiodinium photopigment chlorophyll a. Coral tissue scattering was on average ~1.9x stronger than the scattering of the skeleton, consistent with the model that corals trap photons by high scattering to enhance absorption by algal pigments, while the lower scattering of the skeleton allows spread of light to otherwise shaded coral tissue areas.
EASY TWO-PHOTON IMAGE-SCANNING MICROSCOPY WITH SPAD ARRAY AND BLIND IMAGE RECONSTRUCTION
Authors: Koho S. V. , Slenders E. , Tortarolo G. , Castello M. , Buttafava M. , Villa F. , Tcarenkova E. , Ameloot M. , Bianchini P. , Sheppard C.J.R. , Diaspro A. , Tosi A. , Vicidomini G. 
Published: February 2019

ABSTRACTTwo-photon excitation (2PE) microscopy is the imaging modality of choice, when one desires to work with thick biological samples, possibly in-vivo. However, the resolution in two-photon microscopy is poor, below confocal microscopy, and the lack of an optical pinhole becomes apparent in complex samples as reduced quality of optical sectioning. Here, we propose a straightforward implementation of 2PE image scanning microscopy (2PE-ISM) that, by leveraging our recently introduced ISM platform – based on a new single-photon avalanche diode array detector – coupled with a novel blind image reconstruction method, is shown to improve the optical resolution, as well as the overall image quality in various test samples. Most importantly, our 2PE-ISM implementation requires no calibration or other input from the user – it works like any old and familiar two-photon system, but simply produces higher resolution images (in real-time). Making the complexity disappear, in our view, is the biggest novelty here, and the key for making 2PE-ISM mainstream.
Evolutionary model of protein secondary structure capable of revealing new biological relationships
Authors: Lai Jhih-Siang , Rost Burkhard , Kobe Bostjan , Bodén Mikael 
Published: February 2019

AbstractAncestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, phylo­genetic analyses of remote homologues must handle extreme amino-acid se­quence diversity resulting from extended periods of evolutionary change. We exploited the wealth of protein structures to develop an evolutionary model based on protein secondary structure. The approach follows the differences between discrete secondary structure states observed in modern proteins and those hypothesised in their immediate ancestors. We implemented maximum likelihood-based phylogenetic inference to reconstruct ancestral secondary structure. The predictive accuracy from the use of the evolutionary model surpasses that of comparative modelling and sequence-based prediction; the reconstruction extracts information not available from modern structures or the ancestral sequences alone. Based on a phylogenetic analysis of multiple protein families, we showed that the model can highlight relationships that are evolutionarily rooted in structure and not evident in amino acid-based analysis.
Drug screens of NGLY1 Deficiency worm and fly models reveal catecholamine, NRF2 and anti-inflammatory pathway activation as clinical approaches
Authors: Iyer Sangeetha , Mast Joshua D. , Tsang Hillary , Rodriguez Tamy P. , DiPrimio Nina , Prangley Madeleine , Sam Feba S. , Parton Zachary , Perlstein Ethan O. 
Published: February 2019

AbstractN-glycanase 1/NGLY1 Deficiency is an ultra-rare and complex monogenic glycosylation disorder that affects fewer than 40 patients globally. NGLY1 Deficiency has been studied in model organisms such as yeast, worms, flies and mice. Proteasomal and mitochondrial homeostasis gene networks are controlled by the evolutionarily conserved transcriptional regulator Nrf1, whose activity requires deglycosylation by NGLY1. Hypersensitivity to the proteasome inhibitor bortezomib is a common phenotype observed in whole animal and cellular models of NGLY1 Deficiency. Here we describe unbiased phenotypic drug screens to identify FDA approved drugs, generally recognized as safe natural products and novel chemical entities that rescue growth and development of NGLY1-deficient worm and fly larvae treated with a toxic dose of bortezomib. We used image-based larval size and number assays for use in screens of a 2,560-member drug repurposing library and a 20,240-member lead discovery library. A total of 91 validated hit compounds from primary invertebrate screens were tested in a human cell line in a NRF2 activity assay. NRF2 is a transcriptional regulator that regulates cellular redox homeostasis and it can compensate for loss of Nrf1. Plant-based polyphenols comprise the largest class of hit compounds and NRF2 inducers. Catecholamines and catecholamine receptor activators comprise the second largest class of hits. Steroidal and non-steroidal anti-inflammatory drugs comprise the third largest class. Only one compound was active in all assays and species: the atypical antipsychotic and dopamine receptor agonist aripiprazole. Worm and fly models of NGLY1 Deficiency validate therapeutic rationales for activation of NRF2 and anti-inflammatory pathways based on results in mice and human cell models and suggest a novel therapeutic rationale for boosting catecholamine levels and/or signaling in the brain.
Probing Ligand and Cation Binding Sites in G-Quadruplex Nucleic Acids by Mass Spectrometry and Electron Photodetachment Dissociation Sequencing
Authors: Paul Dababrata , Marchand Adrien , Verga Daniela , Teulade-Fichou Marie-Paule , Bombard Sophie , Rosu Frédéric , Gabelica Valérie 
Published: February 2019

ABSTRACTMass spectrometry provides exquisite detail on ligand and cation binding stoichiometries with a DNA target. The next important step is to develop reliable methods to determine the cation and ligand binding sites in each complex separated by the mass spectrometer. To circumvent the caveat of ligand derivatization for cross-linking, which may alter the ligand binding mode, we explored a tandem mass spectrometry (MS/MS) method that does not require ligand derivatization, and is therefore also applicable to localize metal cations. By obtaining more negative charge states for the complexes using supercharging agents, and by creating radical ions by electron photodetachment, oligonucleotide bonds become weaker than the DNA-cation or DNA-ligand noncovalent bonds upon collision-induced dissociation of the radicals. This electron photodetachment (EPD) method allows to locate the binding regions of cations and ligands by top-down sequencing of the oligonucleotide target. The very potent G-quadruplex ligands 360A and PhenDC3 were found to replace a potassium cation and bind close to the central loop of 4-repeat human telomeric sequences.
Parasites Mediate Condition-Dependent Sexual Selection for Local Adaptation in a Natural Insect Population
Authors: Gómez-Llano Miguel , Narasimhan Aaditya , Svensson Erik I. 
Published: February 2019

ABSTRACTCondition-dependent sexual selection has been suggested to reduce mutation load, and sexual selection might also accelerate local adaptation and promote evolutionary rescue through several ecological and genetic mechanisms. Research on condition-dependent sexual selection has mainly been performed in laboratory settings, while data from natural populations are lacking. One ecological factor that can cause condition-dependent sexual selection is parasitism. Here, we quantified ectoparasite load (Arrenurus water mites) in a natural population of the common bluetail damselfly (Ischnura elegans) over 15 years. We estimated parasite-mediated sexual selection in both sexes and investigated how parasite resistance and tolerance changed over time and influenced population density. Parasites reduced mating success in both sexes, but the effects were stronger in males than in females. The male fitness advantage of carrying fewer parasites was higher under experimental low-density conditions than under high-density field conditions, suggesting that male-male competition could reduce parasite-mediated sexual selection. We further show that population density declined during the study period, while parasite resistance and male fitness tolerance (fecundity) increased, suggestive of increasing local adaptation against parasites and ongoing evolutionary rescue. We suggest that condition-dependent sexual selection can facilitate population persistence and promote evolutionary rescue by increasing local adaptation against parasites.
Multi-objective multi-facility green manufacturing closed-loop supply chain under uncertain environment
Authors: Karimi Behzad , Niknamfar Amir Hossein , Hassan Gavyar Babak , Barzegar Majid , Mohtashami Ali 
Published: February 2019

Purpose
Today’s, supply chain production and distribution of products to improve the customer satisfaction in the shortest possible time by paying the minimum cost, has become the most important challenge in global market. On the other hand, minimizing the total cost of the transportation and distribution is one of the critical items for companies. To handle this challenge, this paper aims to present a multi-objective multi-facility model of green closed-loop supply chain (GCLSC) under uncertain environment. In this model, the proposed GCLSC considers three classes in case of the leading chain and three classes in terms of the recursive chain. The objectives are to maximize the total profit of the GCLSC, satisfaction of demand, the satisfactions of the customers and getting to the proper cost of the consumers, distribution centers and recursive centers.

Design/methodology/approach
Then, this model is designed by considering several products under several periods regarding the recovery possibility of products. Finally, to evaluate the proposed model, several numerical examples are randomly designed and then solved using non-dominated sorting genetic algorithm and non-dominated ranking genetic algorithm. Then, they are ranked by TOPSIS along with analytical hierarchy process so-called analytic hierarchy process-technique for order of preference by similarity to ideal solution (AHP-TOPSIS).

Findings
The results indicated that non-dominated ranked genetic algorithm (NRGA) algorithm outperforms non-dominated sorting genetic algorithm (NSGA-II) algorithm in terms of computation times. However, in other metrics, any significant difference was not seen. At the end, to rank the algorithms, a multi-criterion decision technique was used. The obtained results of this method indicated that NSGA-II had better performance than ones obtained by NRGA.

Originality/value
This study is motivated by the need of integrating the leading supply chain and retrogressive supply chain. In short, the highlights of the differences of this research with the mentioned studies are as follows: developing multi-objective multi-facility model of fuzzy GCLSC under uncertain environment and integrating the leading supply chain and retrogressive supply chain.
Does real exchange rate devaluation improve the current account balance of highly indebted low income countries?
Authors: Ayele Getaneh Mihret 
Published: February 2019

Purpose
The purpose of this paper is to examine whether real exchange rate devaluation improves the current account balance of four highly indebted low-income countries of East Africa.

Design/methodology/approach
The pooled mean group (PMG) approach is used for panel data from four countries over the period 1970–2016. The paper also applied bound testing and ARDL model for time-series data from individual sample countries.

Findings
The panel PMG/ARDL estimation result reveals that real exchange rate devaluation has no significant impact on the current account balance, both in the short and long run. However, the time-series analysis using the bound testing and restricted ARDL estimation suggests that real exchange rate devaluation improves the current account balance in the long run for only Ethiopia. The overall empirical results reveal that the current account balance would improve with the rising domestic income while it deteriorates with increasing foreign income and external indebtedness in the long run.

Originality/value
The paper is original.
Understanding consumer ethics in China’s demographic shift and social reforms
Authors: Chen Wei-Fen , Wang Xue , Gao Haiyan , Hong Ying-Yi 
Published: February 2019

PurposeThe purpose of this paper is to explore some specific, current social phenomena in China that may influence consumers’ ethical beliefs and practices, focusing on how some top-down, social and political changes could shape consumer behavior that needs to be understood in the Chinese context.Design/methodology/approachExtensive literature was critically reviewed to explore recent macro-societal reforms in China and their impact on consumers’ (un)ethical practices.FindingsThe authors lay out how China, a government-led society, underwent a series of political reforms resulting in demographic shifts that differentiate it from its western, industrialized counterparts. The authors connect these societal changes with Chinese characteristics to consumers’ ethical evaluations, forming a new angle to understand consumer ethics in China. The authors also draw on two empirical examples to illustrate the argument.Originality/valueWhile consumer ethics are often explained by either cultural factors or individual variations, the authors discuss how one’s ethical practice is shaped by one’s social position, which is a product of national-level public policy. The discussions have ramifications for the study of consumers’ social class and ethical practices because they take into account the elusive social positions and ambiguous social class consciousness of the Chinese population that have resulted from social mobility. The discussions may give practitioners a better understanding of the ethical rationale behind consumers’ changing lifestyles especially in the Chinese context.
The importance of CSR initiatives in building customer support and loyalty
Authors: Ajina Ahmed Suhail , Japutra Arnold , Nguyen Bang , Syed Alwi Sharifah Faridah , Al-Hajla Ali H. 
Published: February 2019

Purpose
The purpose of this paper is to examine how the perception of CSR influences different aspects of consumer behaviour, specifically focussing on the antecedents of perceived value, customer support and loyalty.

Design/methodology/approach
A total of 418 completed responses were obtained and provided the data to analyse and test the hypothesised research model. To test the hypotheses, structural equation modelling using PLS was employed.

Findings
Findings reveal that customer awareness of the current CSR initiatives to different stakeholder groups significantly influences their perceptions of what social initiatives are actually undertaken by firms for their economic, legal, ethical and philanthropic responsibility. In addition, customer views of what firms actually do in respect to social initiatives are significantly related to their level of CSR expectations. This indicates that the customers will always expect more from banks compared to what they actually do. Surprisingly, CSR perception is not directly related to customers’ loyalty, which contradicts the majority of previous studies indicating that CSR perception influences consumer behaviour.

Originality/value
This study provides an original contribution to the CSR body of knowledge, especially for developing countries where the awareness level is low. It also provides a deep understanding of the influence of CSR into consumer behaviour, as it investigates the influence of the full construct of CSR into customer loyalty. Finally, the study investigated the relationship between the perception and the expectation of CSR; this relationship has been neglected in previous studies, where either CSR perceptions or CSR expectations have been examined separately.
The reasoning behind infrastructure manager’s choice of procurement instruments
Authors: Plantinga Henrico , Voordijk Hans , Doree Andre 
Published: February 2019

Purpose
The purpose of this paper is to show that for frequently procuring public clients: the reasoning behind the use of procurement instruments is a process in its own right that requires managerial and scientific attention; modeling this process contributes to making sensible procurement choices; and managing this process is a relevant factor in the client’s development toward strategic procurement.

Design/methodology/approach
A model is developed to conceptualize the reasoning behind procurement instruments. Using this model in a case study, the reasoning behind the evolution of a particular procurement instrument as applied by a public infrastructure management organization is reconstructed.

Findings
The case study results show that an initially explicitly formulated set of main reasons for operating a qualification system can implicitly evolve over time into a different set of reasons. From a managerial point of view, explication of implicit reasons is important to both avoid the risk that the real value of the procurement instrument remains undetected as well as properly assess its strategic alignment with higher level strategies. The conceptual model proves to be a useful tool to support that.

Originality/value
Bringing the reasoning behind the use of procurement instruments to the fore, this study explores an area of construction procurement research that is positioned between the disciplines of purchasing and supply management, knowledge management and strategic management.
Biases in construction project dispute resolution
Authors: Cheung Sai On , Li Keyao 
Published: February 2019

PurposeThis study aims to propose a framework of bias in construction project dispute resolution (CPDR hereafter).Design/methodology/approachWith reference to the literatures on effects of bias, manifestations of bias in CPDR were developed. Based on data obtained from construction professionals about their frequency of having these bias manifestations, the underlying constructs of biased behaviors were explored by a principal component factor analysis. A confirmatory factor analysis was further conducted to validate the framework of bias in CPDR.FindingsFour types of bias were identified as the constructs that underlie biased behaviors in CPDR. These four biases were included in the bias framework proposed: preconception, self-affirmation, optimism and interest-oriented. The potency of these types of bias was also evaluated.Practical implicationsFirst, the findings inform that the existence of bias in CPDR is real. Early detection allows management to intervene and steer CPDR team back to rational courses. Second, this study suggests optimizing CPDR procedures to diminish the chance of bias occurring.Originality/valueBias is almost an uncharted area in CPDR. The study fills this research gap by conceptualizing the underlying constructs of biased behaviors. The findings inform construction professionals of the likelihood of practicing biased behaviors in CPDR. Repeated dispute decisions in the commonly used multi-tiered dispute resolution process would enable the creeping in of biases.