bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform
Authors: Pichler Monica , Coskun Ömer K. , Ortega Ana Sofia , Conci Nicola , Wörheide Gert , Vargas Sergio , Orsi William D. 
Published: December 2017

ABSTRACTHigh-throughput sequencing of the 16S rRNA gene is widely used in microbial ecology, with Illumina platforms being widely used in recent studies. The MiniSeq, Illumina’s latest benchtop sequencer, enables more cost-efficient DNA sequencing relative to larger sequencing platforms (e.g. MiSeq). Here we used a modified custom primer sequencing approach to test the fidelity of the MiniSeq for high-throughput sequencing of the V4 hypervariable region of 16S rRNA genes from complex communities in environmental samples. To this end, we designed an additional sequencing primer that enabled application of a dual-index barcoding method on the MiniSeq. A mock community was sequenced alongside the environmental samples as a quality control benchmark. After careful filtering procedures, we were able to recapture a realistic richness of the mock community, and identify meaningful differences in alpha and beta diversity in the environmental samples. These results show that the MiniSeq can produce similar quantities of high quality V4 reads compared to the MiSeq, yet is a cost-effective option for any laboratory interested in performing high-throughput 16S rRNA gene sequencing.IMPORTANCEWe modified a custom sequencing approach and used a mock community to test the fidelity of high-throughput sequencing on the Illumina MiniSeq platform. Our results show that the MiniSeq can produce similar quantities of high quality V4 reads compared to the MiSeq. In addition, our protocol increases feasibility for small laboratories to perform their own high-throughput sequencing of the 16S rRNA marker gene.
Suppression of the dihydrolipoamide dehydrogenase gene (dld-1) protects against the toxicity of human amyloid beta inC. elegansmodel of Alzheimer’s disease
Authors: Ahmad Waqar 
Published: December 2017

AbstractDeclines in energy metabolism and associated mitochondrial enzymes are linked to the progression of Alzheimer’s disease (AD). Dihydrolipoamide dehydrogenase (dld) and two of its enzyme complexes namely, pyruvate dehydrogenase and α-ketoglutarate dehydrogenase are associated with AD and have a significant role in energy metabolism. Interestingly,dldgene variants are genetically linked to late-onset AD; and reduced activity of DLD-containing enzyme complexes has been observed in AD patients. To understand how energy metabolism influences AD progression, we suppressed thedld-1gene inC. elegansexpressing the human Aβ peptide.dld-1gene suppression improved many aspects of vitality and function directly affected by Aβ pathology inC. elegans.This includes protection against paralysis, improved fecundity and improved egg hatching rates. Suppression of thedld-1gene restores normal sensitivity to aldicarb, levamisole and serotonin, and improves chemotaxis. Suppression ofdld-1does not decrease levels of the Aβ peptide, but does reduce the formation of toxic Aβ oligomers. The mitochondrial uncoupler, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP) acts synergistically with Aβ to overcome the protective effect ofdld-1gene suppression. Another metabolic toxin, phosphine, acted additively with Aβ. Our work supports the hypothesis that lowering energy metabolism may protect against Aβ pathogenicity, but that this may increase susceptibility to other metabolic disturbances.
Collective cell behaviour in mechanosensing of substrate thickness
Authors: Tusan CG , Man YH , Zarkoob H , Johnson DA , Andriotis OG , Thurner PJ , Yang S , Sander EA , Gentleman E , Sengers BG , Evans ND 
Published: December 2017

AbstractExtracellular matrix stiffness has a profound effect on the behaviour of many cell types. Adherent cells apply contractile forces to the material on which they adhere, and sense the resistance of the material to deformation – its stiffness. This is dependent on both the elastic modulus and the thickness of the material, with the corollary that single cells are able to sense underlying stiff materials through soft hydrogel materials at low (<10 µm) thicknesses. Here, we hypothesised that cohesive colonies of cells exert more force and create more hydrogel deformation than single cells, therefore enabling them to mechanosense more deeply into underlying materials than single cells. To test this, we modulated the thickness of soft (1 kPa) elastic ECM-functionalised polyacrylamide hydrogels adhered to glass substrates and allowed colonies of MG63 cells to form on their surfaces. Cell morphology and deformations of fluorescent fiducial-marker labelled hydrogels were quantified by time-lapse fluorescence microscopy imaging. Single cell spreading increased with respect to decreasing hydrogel thickness, with data fitting to an exponential model with half-maximal response at a thickness of 3.2 μm. By quantifying cell area within colonies of defined area, we similarly found that colony-cell spreading increased with decreasing hydrogel thickness but with a greater halfmaximal response at 54 μm. Depth-sensing was dependent on ROCK-mediated cellular μ contractility. Surface hydrogel deformations were significantly greater on thick hydrogels compared to thin hydrogels. In addition, deformations extended greater distances from the periphery of colonies on thick hydrogels compared to thin hydrogels. Our data suggest that by acting collectively, cells mechanosense rigid materials beneath elastic hydrogels at greater depths than individual cells. This raises the possibility that the collective action of cells in colonies or sheets may allow cells to sense structures of differing material properties at comparatively large distances.
Time-resolved analyses of elemental distribution and concentration in living plants: An example using manganese toxicity in cowpea leaves
Authors: Blamey F. Pax C. , Paterson David J. , Walsh Adam , Afshar Nader , McKenna Brigid A. , Cheng Miaomiao , Tang Caixan , Horst Walter J. , Menzies Neal W. , Kopittke Peter M. 
Published: December 2017

SummaryKnowledge of elemental distribution and concentration within plant tissues is crucial in the understanding of almost every process that occurs within plants. However, analytical limitations have hindered the microscopic determination of changes over time in the location and concentration of nutrients and contaminants in living plant tissues.We developed a novel method using synchrotron-based micro X-ray fluorescence (μ-XRF) that allows for laterally-resolved, multi-element, kinetic analyses of plant leaf tissues in vivo. To test the utility of this approach, we examined changes in the accumulation of Mn in unifoliate leaves of 7-d-old cowpea (Vigna unguiculata) plants grown for 48 h at 0.2 and 30 μM Mn in solution.Repeated μ-XRF scanning did not damage leaf tissues demonstrating the validity of the method. Exposure to 30 μM Mn for 48 h increased the initial number of small spots of localized high Mn and their concentration rose from 40 to 670 mg Mn kg-1 fresh mass. Extension of the two-dimensional μ-XRF scans to a three-dimensional geometry provided further assessment of Mn localization and concentration.This method shows the value of synchrotron-based μ-XRF analyses for time-resolved in vivo analysis of elemental dynamics in plant sciences.
The Brain/MINDS 3D digital marmoset brain atlas
Authors: Woodward Alexander , Hashikawa Tsutomu , Maeda Masahide , Kaneko Takaaki , Hikishima Keigo , Iriki Atsushi , Okano Hideyuki , Yamaguchi Yoko 
Published: December 2017

AbstractWe present a new 3D digital brain atlas of the non-human primate, common marmoset monkey (Callithrix jacchus), with MRI and coregistered Nissl histology data. To the best of our knowledge this is the first comprehensive digital 3D brain atlas of the common marmoset having normalized multi-modal data, cortical and sub-cortical segmentation, and in a common file format (NIfTI). The atlas can be registered to new data, is useful for connectomics, functional studies, simulation and as a reference.The atlas was based on previously published work but we provide several critical improvements to make this release valuable for researchers. Nissl histology images were processed to remove illumination and shape artifacts and then normalized to the MRI data. Brain region segmentation is provided for both hemispheres. The data is in the NIfTI format making it easy to integrate into neuroscience pipelines, whereas the previous atlas was in an inaccessible file format. We also provide cortical, mid-cortical and white matter boundary segmentations useful for visualization and analysis.
A zinc-finger fusion protein refines Gal4-defined neural circuits
Authors: Raghu Shamprasad Varija , Mohammad Farhan , Yi Chua Jia , Barros Claudia S. , Lam Joanne , Loberas Mavis , Sahani Sadhna , Claridge-Chang Adam 
Published: December 2017

AbstractThe analysis of behavior requires that the underlying neuronal circuits are identified and genetically isolated. In several major model species—most notablyDrosophila, neurogeneticists identify and isolate neural circuits with a binary heterologous expression-control system: Gal4–UASG. One limitation of Gal4–UASG is that expression patterns are often too broad to map circuits precisely. To help refine the range of Gal4 lines, we developed an intersectional genetic AND operator. Interoperable with Gal4, the new system’s key component is a fusion protein in which the DNA-binding domain of Gal4 has been replaced with a zinc finger domain with a different DNA-binding specificity. In combination with its cognate binding site (UASZ) thezinc-finger-replaced Gal4 (‘Zal1’) was functional as a standalone transcription factor. Zal1 transgenes also refined Gal4 expression ranges when combined with UASGZ, a hybrid upstream activation sequence. In this way, combining Gal4 and Zal1 drivers captured restricted cell sets compared with single drivers and improved genetic fidelity. This intersectional genetic AND operation presumably derives from the action of a heterodimeric transcription factor: Gal4-Zal1. Configurations of Zal1–UASZ and Zal1-Gal4-UASGZ are versatile tools for defining, refining, and manipulating targeted neural expression patterns with precision.
Recovery of equilibrium free energy from non-equilibrium thermodynamics with mechanosensitive ion channels inE. coli
Authors: Çetiner Uğur , Raz Oren , Sukharev Sergei , Jarzynski Christopher 
Published: December 2017

AbstractBacterial mechanosensitive channels are major players in cells’ ability to cope with hypo-osmotic stress. Excess turgor pressure due to fast water influx is reduced as the channels, triggered by membrane tension, open and release osmolytes. However,in vitromeasurements of the free energy difference between the open and closed states of ion channels are challenging due to hysteresis effects and inactivation. Exploiting recent developments in statistical physics, we present a general formalism to extract the free energy difference between the closed and open states of mechanosensitive ion channels from non-equilibrium work distributions associated with the channels’ gating recorded in native patches under ramp stimulation protocols. We show that the work distributions obtained from the gating of MscS channels inE. colimembrane satisfy the strong symmetry relations predicted by the fluctuation theorems and recover the equilibrium free energy difference between the closed and open states of the channel within 1 kBT of its best estimate obtained from an independent experiment.
Estimating global enzyme abundance levels from cofactor requirements: a model-based analysis of the iron metabolism in yeast
Authors: Dikicioglu Duygu , Oliver Stephen G. 
Published: December 2017

SummaryMetabolic networks adapt to changes in their environment by modulating the activity of their enzymes and transporters; often by changing their abundance. Understanding such quantitative changes can shed light onto how metabolic adaptation works, or how it can fail and lead to a metabolically dysfunctional state. Unfortunately such data are only available on a fraction of the enzyme and transporter pools, and this leaves us distant from generating the full picture. We here propose a strategy to quantify metabolic protein requirements for cofactor-bearing enzymes and transporters through constraint-based modelling. In this work, we constructed the first eukaryotic genome-scale metabolic model with a comprehensive iron metabolism and investigated partial functional impairment of the genes involved in iron-sulphur (Fe-S) cluster maturation, which revealed extensive rewiring of the fluxes in silico, despite only marginal phenotypic dissimilarities. The yeast metabolism at steady state was determined to employ a constant iron-recruiting enzyme turnover at a rate of 3.02 × 10−11 mM / (g biomass)−1 h−1. Furthermore, we employed this model to identify and study a mutualistic relationship between Streptomyces coelicolor and Saccharomyces cerevisiae, which involves iron and folate sharing economies between the two microbes.
Critical factors for transferring and sharing tacit knowledge within lean and agile construction processes
Authors: Saini Mandeep , Arif Mohammed , Kulonda Dennis J. 
Published: December 2017

Purpose
The purpose of the paper is to investigate the critical success factors (CSFs) associated with the effectiveness of transfer and sharing of tacit knowledge in lean and agile construction processes.

Design/methodology/approach
The study identifies ten CSFs that initiate the transferring and sharing of tacit knowledge. The CSFs are validated through quantitative study. This study recruited project managers, executives, consultants and other managers that are directly involved in the management of a construction project. It recruits the respondents those have background and experience from disciplines such as lean construction, agile construction, construction supply chain (CSC) and knowledge management in lean, agile and CSC. The data collected through self-administrative questionnaire are categorised as ordinal data to analyse in SPSS with frequency and Kruskal–Wallis H test, Spearman’s correlation analysis and a rank-order analysis is done to establish the level of importance of those factors.

Findings
Initially, “Trust between construction organisations” is identified as the foremost CSF. Moreover, other CSFs such as motivation, leadership capabilities, business strategies and organisational capabilities follow trust.

Originality/value
This is the first study that investigates and establishes the CSFs that are essential to initiate transferring and sharing tacit knowledge in a lean and in an agile construction processes.
Long-run drivers and short-term dynamics of Swedish real house prices
Authors: Asal Maher 
Published: December 2017

PurposeThis paper aims to assess the long-run drivers and short-term dynamics of real house prices in Sweden for 1986Q1 to 2016Q4. More specifically, the author examines the extent to which real house prices are determined by affordability, demographics and asset price factors.Design/methodology/approachThe author conducts a cointegration analysis and applies a vector autoregression model to examine the long- and short-run responsiveness of Swedish real house prices to a number of key categories of fundamental variables.FindingsThe empirical results indicate that house prices will increase in the long run by 1.04 per cent in response to a 1 per cent increase in household real disposable income, whereas real after-tax mortgage interest and real effective exchange rates show average long-term effects of approximately – 8 and – 0.7 per cent, respectively. In addition, the results show that the growth of real house prices is affected by growth in mortgage credit, real after-tax mortgage interest rates and disposable incomes in the short run, whereas the real effective exchange rate is the most significant determinant of Swedish real house appreciation.Originality/valueThe impact of the two lending restrictions been implemented after the financial crisis – the mortgage cap in October 2010 and the amortization requirement in June 2016 – are ineffective to stabilize the housing market. This suggests that macroprudential measures designed to ease pressure on housing prices and reduce risks to financial stability need to focus on these fundamentals and address the issues of tax deductibility on mortgage rates and the gradual implementation of debt-to-income limits to contain mortgage demand and improve households’ resilience to shocks.
CEO pay-risk sensitivity, firm policies, and 2009 Australian tax reforms
Authors: Bian Chao , Gan Christopher , Li Zhaohua , Hu Baiding 
Published: December 2017

PurposeThe purpose of this paper is to examine the effects of chief executive officer (CEO) vega on firm policies in the Australian share market based on a panel data set drawn from the 137 Australian public firms for the period 2003-2012.Design/methodology/approachTo allow mutual causation between our variables, the authors use the two-stage least squares estimation method, controlling for firm fixed effects. The authors use the difference-in-differences model to test whether the 2009 Australian tax reforms may discourage high-vega CEOs to take value-enhancing risks.FindingsThe authors find the evidence that vega induces CEOs to adopt the riskier financial policy in the Australian capital market. This evidence is further supported by the negative association between vega and firm conservative activities including cash and hedging policies. Further, the result shows that the 2009 tax reforms reduce the CEOs’ willingness to engage in risky financial policy. This finding implies that regulators may restore the 2009 reforms’ “deferred tax point” back to its pre-2009 form.Originality/valueBased on the study’s results, firms should grant CEOs more out-of-the money options with a longer time to expiration to offset the 2009 tax reforms’ negative impact on the CEO’s incentive to take value-enhancing risks.
Liderazgo orientado a la gente encall centers
Authors: León Federico R. , Morales Oswaldo , Ramos Juan D. , Goyenechea Álvaro , Rojas Paul A. , Meza José , Burga-León Andrés 
Published: December 2017

PurposeCall centers generate stress and absenteeism in staff and the literature suggests that people-oriented leadership is the right way of supervision for such a situation. This study compared its effects versus those of other types of leadership.MethodologyAbsentee data of 379 representatives of customer services of a Peruvian call center were analyzed and the representatives answered a questionnaire about the Framework of Values in Competition and its four types of leadership. Day and night work shifts were compared.ResultsIt was observed that absenteeism declines with people-oriented leadership, although only during the day shift, and the addition of leadership oriented to change, results and control devalues models.Limitations/implicationsFuture studies should cover the performance of the worker. The findings suggest a need to re-focus the theoretical focus on environmental contingencies that affect leadership effectiveness.Originality/valueLeadership theorists will ask themselves in what circumstances the multiple leadership is effective. Call center managers will appreciate the organizational value of people-oriented leadership at the first level of supervision.
Social vs traditional media communication: brand origin associations strike a chord
Authors: Morra Maria Cristina , Ceruti Francesca , Chierici Roberto , Di Gregorio Angelo 
Published: December 2017

Purpose
The purpose of this study is to develop an analytical comparison between the impact of social media communication (both user-generated and firm-created) and the effects of traditional media communication. In particular, the components of customer-based brand equity and any difference in the effects according to brand origin associations are investigated. The target group consisted of fans and followers of beer brands on social media.

Design/methodology/approach
In all, 192 questionnaires were collected a survey link that was posted on beer brand pages that operate in the Italian market. Structural equation modeling was developed to investigate the impact of social and traditional media communication on brand equity and a multi-group analysis to examine the differences according to the brand names’ origin associations.

Findings
Results show that fans and followers cannot be considered as a collective unit. Additionally, consumers make a clear distinction between firm-created/user-generated social media and traditional media communication. Specifically, they distinguish how the effects of the two media outlets differ in relation to the brand origin associations. International brands should concentrate on both firm-created and user-generated communication, whereas national (Italian) brands should foster their firm-created communications. In both cases, however, traditional media communication loses its effectiveness on the brand equity components.

Originality/value
Contrary to existing literature, this project compares the effect of 2.0 and traditional media on various social media platforms, pointing out two different models according to the brands’ origin associations. This study develops interesting insights both for international companies with huge brand portfolios and for national firms in a complex market like those for beer.