bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone, Nematostella vectensis
Authors: Karabulut Ahmet , He Shuonan , Chen Cheng-Yi , McKinney Sean A. , Gibson Matthew C. 
Published: September 2018

ABSTRACTA mechanistic understanding of evolutionary developmental biology requires the development of novel techniques for the manipulation of gene function in phylogenetically diverse organismal systems. Recently, gene-specific knockdown by microinjection of short hairpin RNA (shRNA) has been applied in the sea anemone Nematostella vectensis, a cnidarian model organism. Due to the unusual architecture of the cnidarian microRNA processing pathway, the shRNA approach is unusually effective for sequence-specific knockdown of a gene of interest. However, the time- and labor-intensive process of microinjection limits access to this technique and its application in large scale experiments. To address this issue, here we present an electroporation protocol for shRNA delivery into Nematostella eggs. This method leverages the speed and simplicity of electroporation, enabling users to manipulate gene expression in hundreds of Nematostella eggs or embryos within minutes. We provide a detailed description of the experimental procedure, including reagents, electroporation conditions, preparation of Nematostella vectensis eggs, and follow-up care of experimental animals. Finally, we demonstrate the knockdown of several endogenous and exogenous genes with known phenotypes and discuss the potential applications of this method.
Thalamocortical dynamics underlying spontaneous transitions in beta power in Parkinsonism
Authors: Reis Carolina , Sharott Andrew , Magill Peter J. , van Wijk Bernadette , Parr Thomas , Zeidman Peter , Friston Karl , Cagnan Hayriye 
Published: September 2018

AbstractParkinson’s disease (PD) is a neurodegenerative condition in which aberrant oscillatory synchronization of neuronal activity at beta frequencies (15-35 Hz) across the cortico-basal ganglia-thalamocortical circuit is associated with debilitating motor symptoms, such as bradykinesia and rigidity. Mounting evidence suggests that the magnitude of beta synchrony in the parkinsonian state fluctuates over time, but the mechanisms by which thalamocortical circuitry regulates the dynamic properties of cortical beta in PD are poorly understood. Using the recently developed generic dynamic causal modelling framework, we recursively optimised a set of plausible models of the thalamocortical circuit (n=144) to infer the neural mechanisms that best explain the transitions between low and high beta power states observed in recordings of field potentials made in the motor cortex of anesthetized Parkinsonian rats. Bayesian model comparison suggests that upregulation of cortical rhythmic activity in the beta-frequency band results from changes in the coupling strength both between and within the thalamus and motor cortex. Specifically, our model indicates that high levels of cortical beta synchrony are mainly achieved by a delayed (extrinsic) input from thalamic relay cells to deep pyramidal cells and a fast (intrinsic) input from middle pyramidal cells to superficial pyramidal cells. We therefore hypothesize that beta synchronisation at the cortical level could selectively be modulated via interventions that are capable of finely regulating cortical excitability in a spatial (delivered to either the superficial or deep cortical laminae) and time specific manner.
How yeast cells find their mates
Authors: Henderson Nicholas T. , Clark-Cotton Manuella R. , Zyla Trevin R. , Lew Daniel J. 
Published: September 2018

AbstractAccurate detection of extracellular chemical gradients is essential for many cellular behaviors. Gradient sensing is challenging for small cells, which experience little difference in ligand concentrations on the up-gradient and down-gradient sides of the cell. Nevertheless, the tiny cells of the yeastSaccharomyces cerevisiaereliably decode gradients of extracellular pheromones to find their mates. By imaging the behavior of polarity factors and pheromone receptors during mating encounters, we found that gradient decoding involves two steps. First, cells bias orientation of initial polarity up-gradient, even though they have unevenly distributed receptors. To achieve this, they measure the local fraction of occupied receptors, rather than absolute number. However, this process is error-prone, and subsequent exploratory behavior of the polarity factors corrects initial errors via communication between mating partners. The mobile polarity sites convert the difficult problem of spatial gradient decoding into the easier one of sensing temporal changes in local pheromone levels.
Optimization of the flash extraction of flavonoids from the leaves ofSalix babylonicausing the response surface method and an evaluation of the leaves’ high antioxidant activity
Authors: Chen Huijie , Diao Lei , Zhang Yue , Liu Haixin , Zhong Ming , Li Guangxing 
Published: September 2018

AbstractMany biological activities ofSalix babylonicaleaves are attributed to the plants’ high total flavonoid content. Flash extraction has the advantages of high efficiency and maximum retention of the active ingredient. In this study, flash extraction was used to extract the total flavonoids, and a Box–Behnken design was used to optimize the extraction conditions for the first time. The effects of four independent variables, including ethanol concentration, extraction voltage, time, and ratio of liquid to material on flavonoid yield, was determined, and the optimal conditions for flavonoid extraction were evaluated using response surface methodology. Statistical analyses showed that the linear and quadratic terms of these four variables had significant effects. The fitted second-order model revealed that the optimal conditions consisted of an ethanol concentration of 67.91%, extraction time of 87 s, extraction voltage of 116 V and ratio of liquid to material of 42.79. Under the optimum conditions, the experimental value of 66.40±0.80% nearly coincided with that predicted by the model. In the ferric reducing antioxidant power (FRAP) and 2,2-diphenyl-1-picrylhydrazyl radical (DPPH.) assays, the extracts showed significant antioxidant and scavenging capacity for free radicals, respectively. This study helps to better exploit the resources ofSalix babylonicaleaves and provides new insights for effective extraction of flavonoids.
Boundaries support specific long-distance interactions between enhancers and promoters inDrosophila Bithoraxcomplex
Authors: Postika Nikolay , Metzler Mario , Affolter Markus , Müller Martin , Schedl Paul , Georgiev Pavel , Kyrchanova Olga 
Published: September 2018

AbstractDrosophilabithorax complex (BX-C) is one of the best model systems for studying the role of boundaries (insulators) in gene regulation. Expression of three homeotic genes,Ubx, abd-A,andAbd-B, is orchestrated by nine parasegment-specific regulatory domains. These domains are flanked by boundary elements, which function to block crosstalk between adjacent domains, ensuring that they can act autonomously. Paradoxically, seven of the BX-C regulatory domains are separated from their gene target by at least one boundary, and must “jump over” the intervening boundaries. To understand the jumping mechanism, theMcpboundary was replaced withFab-7andFab-8.Mcpis located between theiab-4andiab-5domains, and defines the border between the set of regulatory domains controllingabd-AandAbd-B. WhenMcpis replaced byFab-7orFab-8,they direct theiab-4domain (which regulatesabd-A) to inappropriately activateAbd-Bin abdominal segment A4. For theFab-8replacement, ectopic induction was only observed when it was inserted in the same orientation as the endogenousFab-8boundary. A similar orientation dependence for bypass activity was observed whenFab-7was replaced byFab-8. Thus, boundaries perform two opposite functions in the context of BX-C – they block crosstalk between neighboring regulatory domains, but at the same time actively facilitate long distance communication between the regulatory domains and their respective target genes.Author SummaryDrosophilabithorax complex (BX-C) is one of a few examples demonstratingin vivorole of boundary/insulator elements in organization of independent chromatin domains. BX-C contains threeHOXgenes, whose parasegment-specific pattern is controlled bycis-regulatory domains flanked by boundary/insulator elements. Since the boundaries ensure autonomy of adjacent domains, the presence of these elements poses a paradox: how do the domains bypass the intervening boundaries and contact their proper regulatory targets? According to the textbook model, BX-C regulatory domains are able to bypass boundaries because they harbor special promoter targeting sequences. However, contrary to this model, we show here that the boundaries themselves play an active role in directing regulatory domains to their appropriateHOXgene promoter.
The effects of age at menarche and first sexual intercourse on reproductive and behavioural outcomes: a Mendelian randomization study
Authors: Lawn Rebecca B , Sallis Hannah M , Wootton Robyn E , Taylor Amy E , Demange Perline , Fraser Abigail , Penton-Voak Ian S , Munafò Marcus R 
Published: September 2018

SummaryThere is substantial variation in the timing of significant reproductive life events such as menarche and first sexual intercourse. Life history theory explains this variation as an adaptive response to the developmental environment. In environments characterized by harsh conditions, adopting a fast life history strategy may increase fitness. In line with this, there is evidence demonstrating that greater childhood adversity is associated with earlier age at menarche. Here we applied Mendelian randomization (MR) methods to investigate whether there is a causal effect of variation in age at menarche and age at first sexual intercourse on outcomes related to reproduction, education and risky behaviour in UK Biobank (N = 114883–181,255). Our results suggest that earlier age at menarche affects some traits that characterize life history strategies including earlier age at first and last birth, decreased educational attainment, and decreased age at leaving education (for example, we found evidence for a 0.26 year decrease in age at first birth per year decrease in age at menarche, 95% confidence interval: −0.34 to −0.17; p < 0.0001). We find no clear evidence of effects of age at menarche on other outcomes, such as risk taking behaviour. Age at first sexual intercourse was also related to many life history outcomes, although there was evidence of horizontal pleiotropy which violates an assumption of MR and results should be treated with caution. Taken together, these results highlight how MR can be applied to test predictions of life history theory and to better understand determinants of health and social behaviour.
Effect of temperature and pressure on mechanical, surface and electrochemical properties of Al-1.5Cu-5.5Zn-2.5Mg (Alumix-431)
Authors: Acar Ayşe Nur , Mutlu Rasiha Nefise , Ekşi Abdul Kadir , Ekicibil Ahmet , Yazıcı Birgül 
Published: September 2018

Purpose
The purpose of this paper is to examine new alloys created from Alumix 431 powder and investigate their mechanical and electrochemical properties.

Design/methodology/approach
In this study; Alumix-431 alloy samples were prepared using the powder metallurgy (P/M) method applying cold (RT) and warm (50°C and 80°C) compaction methods under pressures of 200 and 250 MPa and were sintered at 600°C in N2(g) atmosphere. Hardness and density of the samples were measured, and corrosion properties were determined by electrochemical impedance spectroscopy charting polarization curves. Surface characterization was determined by contact angle, scanning electron microscopy/mapping, energy dispersive X-ray spectrometry and X-ray diffractometry images.

Findings
Alumix-431 alloys obtained upon compaction at 250 MPa/50 °C had the highest mechanical properties and corrosion resistance and good surface properties. On the surfaces of Alumix-431 alloys, α-Al, MgZn2, Al2,CuMg, Al2,O3, Al2MgO4 phases were recorded.

Originality/value
This study aimed to construct a correlation between mechanical and electrochemical properties of the newly created alloys (prepared under special conditions).
Continuous process improvement implementation framework using multi-objective genetic algorithms and discrete event simulation
Authors: Kang Parminder Singh , Bhatti Rajbir Singh 
Published: September 2018

Purpose
Continuous process improvement is a hard problem, especially in high variety/low volume environments due to the complex interrelationships between processes. The purpose of this paper is to address the process improvement issues by simultaneously investigating the job sequencing and buffer size optimization problems.

Design/methodology/approach
This paper proposes a continuous process improvement implementation framework using a modified genetic algorithm (GA) and discrete event simulation to achieve multi-objective optimization. The proposed combinatorial optimization module combines the problem of job sequencing and buffer size optimization under a generic process improvement framework, where lead time and total inventory holding cost are used as two combinatorial optimization objectives. The proposed approach uses the discrete event simulation to mimic the manufacturing environment, the constraints imposed by the real environment and the different levels of variability associated with the resources.

Findings
Compared to existing evolutionary algorithm-based methods, the proposed framework considers the interrelationship between succeeding and preceding processes and the variability induced by both job sequence and buffer size problems on each other. A computational analysis shows significant improvement by applying the proposed framework.

Originality/value
Significant body of work exists in the area of continuous process improvement, discrete event simulation and GAs, a little work has been found where GAs and discrete event simulation are used together to implement continuous process improvement as an iterative approach. Also, a modified GA simultaneously addresses the job sequencing and buffer size optimization problems by considering the interrelationships and the effect of variability due to both on each other.
Stakeholder management: a systematic literature review
Authors: Pedrini Matteo , Ferri Laura Maria 
Published: September 2018

PurposeThe stakeholder theory is a prominent management approach that has primarily been adopted in the past few years. Despite the increase in the theory’s use, a limited number of studies have discussed ways to develop, execute and measure the results of using this strategic approach with stakeholders. This study aims to address this gap in the literature by conducting a systematic review of the stakeholder management process.Design/methodology/approachFive databases were selected to search articles published from 1985 to 2015. The keywords used were stakeholder management, stakeholder relationship and stakeholder engagement. Starting from 2,457 articles identified using a keyword search, 33 key journal articles were systematically reviewed using both bibliometric and qualitative methods for analysis.FindingsThe results highlight that stakeholder management is increasingly embedded in corporate activities, and that the coming of the internet, social networking and Big Data have put more pressure on companies to develop new tools and techniques to manage stakeholders online. In conclusion, synthesizing the findings and developed framework allows the understanding of different streams of research and identifies future steps for research.Originality/valueWhile literature reviews are a widespread practice in business studies, only a few more recent reviews use the systematic review methodology that aggregates knowledge using clearly defined processes and criteria. This is the first review on stakeholder management in which the structure is existing knowledge on strategy development, execution and the measurement of performance.
Voltage distribution in the windings of high temperature inverter-fed motors
Authors: Roger Daniel , Napieralska-Juszczak Ewa 
Published: September 2018

Purpose
High-temperature (HT°) motors are made with inorganic coils wound with a ceramic-coated wire. They must be carefully designed because the HT° insulating materials have a lower breakdown voltages than the polymers used for insulating standard machines.

Design/methodology/approach
The voltage distribution between stator coils is computed with high-frequency (HF) equivalent circuits that consider the magnetic couplings and the stray capacitances. Two time scales are used for getting a fast computation of very short voltage spikes. For the first step, a medium time scale analysis is performed considering a simplified equivalent circuit made without any stray capacitance but with the full PWM pattern and the magnetic couplings. For the second step, a more detailed HF equivalent circuit computes voltage spikes during short critical time windows.

Findings
The computation made during the first step provides the critical time windows and the initial values of the state variables to the second one. The rise and fall time of the electronic switches have a minor influence on the maximum voltage stress. Conversely, the connection cable length and the common-mode capacitances have a large influence.

Research limitations/implications
HF equivalent circuits cannot be used with random windings but only to formed coils that have a deterministic position of turns.

Practical implications
The proposed method can be used designing of HT° machine windings fed by PWM inverter and for improving the coils of standard machine used in aircraft’s low-pressure environments.

Originality/value
The influence of grounding system of the DC link is considered for computing the voltage spikes in the motor windings.
Finding a place for genealogy and family history in the digital humanities
Authors: Hoeve Casey Daniel 
Published: September 2018

Purpose
Despite its growing popularity, there is a noticeable absence of references to the inclusion of genealogy and family history studies within the field of digital humanities. New forms of inclusiveness, particularly in production-coding and cultural analysis, closely align genealogy and family history with the core tenants practiced among humanities computing and digital humanities. This paper aims to prove that genealogy as family history should be formally recognized within this cohort, as it can serve as a valuable and innovative partner for advocacy and technological advancement of the field.

Design/methodology/approach
By examining the literature, genealogy will be defined according to its use in the digital humanities, as well as its use in family history studies. The core tenants of humanities computing and digital humanities will be identified and compared against the research methodology and technological tools used in genealogy and family history research. The comparison will determine how closely the fields align, and if genealogy defined as family history should be used, and included within the field of digital humanities.

Findings
The progression of genealogy and family history from production to cultural analysis corresponds with the transition of production and coding (influenced by humanities computing) to the inclusion of experimental cultural research adopted by the digital humanities. Genealogy’s use of technological tools, such as databases, text encoding, data-text mining, graphic information systems and DNA mapping, demonstrates the use of coding and production. Cultural analysis through demographic study, crowdsourcing and establishing cultural connections illustrates new methods of scholarship, and connects coding and cultural criticism, serving as a bridge between digital humanities and the humanities at large. As genealogy continues to create new partnerships of a collaborative nature, it can, and will, continue to contribute to new areas of study within the field. As these practices continue to converge with the digital humanities, genealogy should be recognized as a partner and member in the digital humanities cohort.

Originality/value
Despite its growing popularity, there is a noticeable absence of references to the inclusion of genealogy and family history studies within the field of the digital humanities. The term genealogy resonates differently within the digital humanities, primarily articulating the history of the field over the study and research of family lineage. This study seeks to demonstrate how genealogy and family history can fit within the digital humanities, providing a new perspective that has not yet been articulated in the scholarly literature.
3D investigation of natural convection of nanofluids in a curved boundary enclosure applying lattice Boltzmann method
Authors: Hosseini Abadshapoori Mehdi , Saidi Mohammad Hassan 
Published: September 2018

Purpose
The purpose of this paper is to investigate the natural convection behavior of nanofluids in an enclosure. The enclosure is a 3D capsule with curved boundaries filled with TiO2-water nanofluid.

Design/methodology/approach
In this paper, a multiple relaxation times lattice Boltzmann method (MRT-LBM) has been used. Two-component LBM has been conducted to consider the interaction forces between nanoparticles and the base fluid.

Findings
Results show that the enhanced Nusselt number (Nu*) increases with the increase in volume fraction of nanoparticles (ϕ) and Ra number and decrease of nanoparticle size (λ). Additionally, the findings indicate that increasing volume fraction beyond a certain value decreases Nu*.

Originality/value
This paper presents a MRT model of lattice Boltzmann in a 3D curved enclosure. A correlation is also presented based on the current results for Nu* depending on Ra number, volume fraction and size of nanoparticles. Furthermore, a comparison for the convergence rate and accuracy of this model and the SIMPLE algorithm is presented.
Factors impacting technology adoption in hospital bed logistics
Authors: Feibert Diana Cordes , Jacobsen Peter 
Published: September 2018

Purpose
The purpose of this paper is to refine and expand technology adoption theory for a healthcare logistics setting by combining the technology–organization–environment framework with a business process management (BPM) perspective. The paper identifies and ranks factors impacting the decision to implement instances of technologies in healthcare logistics processes.

Design/methodology/approach
A multiple case study is carried out at five Danish hospitals to investigate the bed logistics process. A combined technology adoption and BPM lens is applied to gain an understanding of the reasoning behind technology adoption.

Findings
A set of 17 factors impacting the adoption of technologies within healthcare logistics was identified. The impact factors perceived as most important to the adoption of technologies in healthcare logistics processes relate to quality, employee work conditions and employee engagement.

Research limitations/implications
This paper seeks to understand how managers can use knowledge about impact factors to improve processes through technology adoption. The findings of this study provide insights about the factors impacting the adoption of technologies in healthcare logistics processes. Differences in perceived importance of factors enable ranking of impact factors, and prioritization of changes to be implemented. The study is limited to five hospitals, but is expected to be representative of public hospitals in developed countries and applicable to similar processes.

Originality/value
The study contributes to the empirical research within the field of BPM and technology adoption in healthcare. Furthermore, the findings of this study enable managers to make an informed decision about technology adoption within a healthcare logistics setting.