bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries
Authors: Cho Namjin , Hwang Byungjin , Yoon Jung-ki , Park Sangun , Lee Joongoo , Seo Han Na , Lee Jeewon , Huh Sunghoon , Chung Jinsoo , Bang Duhee 
Published: September 2015

AbstractInterpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.
Neuronal and behavioural modulations by pathway-selective optogenetic stimulation of the primate oculomotor system
Authors: Inoue Ken-ichi , Takada Masahiko , Matsumoto Masayuki 
Published: September 2015

AbstractOptogenetics enables temporally and spatially precise control of neuronal activity in vivo. One of the key advantages of optogenetics is that it can be used to control the activity of targeted neural pathways that connect specific brain regions. While such pathway-selective optogenetic control is a popular tool in rodents, attempts at modulating behaviour using pathway-selective optogenetics have not yet been successful in primates. Here we develop a methodology for pathway-selective optogenetics in macaque monkeys, focusing on the pathway from the frontal eye field (FEF) to the superior colliculus (SC), part of the complex oculomotor network. We find that the optogenetic stimulation of FEF projections to the SC modulates SC neuron activity and is sufficient to evoke saccadic eye movements towards the response field corresponding to the stimulation site. Thus, our results demonstrate the feasibility of using pathway-selective optogenetics to elucidate neural network function in primates.
Enhanced Power Output of a Triboelectric Nanogenerator Composed of Electrospun Nanofiber Mats Doped with Graphene Oxide
Authors: Huang Tao , Lu Mingxia , Yu Hao , Zhang Qinghong , Wang Hongzhi , Zhu Meifang 
Published: September 2015

AbstractWe developed a book-shaped triboelectric nanogenerator (TENG) that consists of electrospun polyvinylidene fluoride (PVDF) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) nanofibers to effectively harvest mechanical energy. The dispersed graphene oxide in the PVDF nanofibers acts as charge trapping sites, which increased the interface for charge storage as well as the output performance of the TENG. The book-shaped TENG was used as a direct power source to drive small electronics such as LED bulbs. This study proved that it is possible to improve the performance of TENGs using composite materials.
Combination of transcriptomic and metabolomic analyses reveals a JAZ repressor in the jasmonate signaling pathway of Salvia miltiorrhiza
Authors: Ge Qian , Zhang Yuan , Hua Wen-Ping , Wu Yu-Cui , Jin Xin-Xin , Song Shuang-Hong , Wang Zhe-Zhi 
Published: September 2015

AbstractJasmonates (JAs) are plant-specific key signaling molecules that respond to various stimuli and are involved in the synthesis of secondary metabolites. However, little is known about the JA signal pathway, especially in economically significant medicinal plants. To determine the functions of novel genes that participate in the JA-mediated accumulation of secondary metabolites, we examined the metabolomic and transcriptomic signatures from Salvia miltiorrhiza. For the metabolome, 35 representative metabolites showing significant changes in rates of accumulation were extracted and identified. We also screened out 2131 differentially expressed unigenes, of which 30 were involeved in the phenolic secondary metabolic pathway, while 25 were in the JA biosynthesis and signal pathways. Among several MeJA-induced novel genes, SmJAZ8 was selected for detailed functional analysis. Transgenic plants over-expressing SmJAZ8 exhibited a JA-insensitive phenotype, suggesting that the gene is a transcriptional regulator in the JA signal pathway of S. miltiorrhiza. Furthermore, this transgenic tool revealed that JAZ genes have novel function in the constitutive accumulation of secondary metabolites. Based on these findings, we propose that the combined strategy of transcriptomic and metabolomic analyses is valuable for efficient discovery of novel genes in plants.
Engineering protein processing of the mammary gland to produce abundant hemophilia B therapy in milk
Authors: Zhao Jianguo , Xu Weijie , Ross Jason W. , Walters Eric M. , Butler Stephen P. , Whyte Jeff J. , Kelso Lindsey , Fatemi Mostafa , Vanderslice Nicholas C. , Giroux Keith , Spate Lee D. , Samuel Melissa S. , Murphy Cliff N. , Wells Kevin D. , Masiello Nick C. , Prather Randall S. , Velander William H. 
Published: September 2015

AbstractBoth the low animal cell density of bioreactors and their ability to post-translationally process recombinant factor IX (rFIX) limit hemophilia B therapy to <20% of the world’s population. We used transgenic pigs to make rFIX in milk at about 3,000-fold higher output than provided by industrial bioreactors. However, this resulted in incomplete γ-carboxylation and propeptide cleavage where both processes are transmembrane mediated. We then bioengineered the co-expression of truncated, soluble human furin (rFurin) with pro-rFIX at a favorable enzyme to substrate ratio. This resulted in the complete conversion of pro-rFIX to rFIX while yielding a normal lactation. Importantly, these high levels of propeptide processing by soluble rFurin did not preempt γ-carboxylation in the ER and therefore was compartmentalized to the Trans-Golgi Network (TGN) and also to milk. The Golgi specific engineering demonstrated here segues the ER targeted enhancement of γ-carboxylation needed to biomanufacture coagulation proteins like rFIX using transgenic livestock.
Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate
Authors: Chen Jun , Shen Jing , Ingvar Hellgren Lars , Ruhdal Jensen Peter , Solem Christian 
Published: September 2015

AbstractLactococcus lactis is essential for most cheese making and this mesophilic bacterium has its growth optimum around 30 °C. We have, through adaptive evolution, isolated a mutant TM29 that grows well up to 39 °C and continuous growth at 40 °C is possible if pre-incubated at a slightly lower temperature. At the maximal permissive temperature for the wild-type, 38 °C, TM29 grows 33% faster and has a 12% higher specific lactate production rate than its parent MG1363, which results in fast lactate accumulation. Genome sequencing was used to reveal the mutations accumulated, most of which were shown to affect thermal tolerance. Of the mutations with more pronounced effects, two affected expression of single proteins (chaperone; riboflavin transporter), two had pleiotropic effects (RNA polymerase) which changed the gene expression profile and one resulted in a change in the coding sequence of CDP-diglyceride synthase. A large deletion containing 10 genes was also found to affect thermal tolerance significantly. With this study we demonstrate a simple approach to obtain non-GMO derivatives of the important L. lactis that possess properties desirable by the industry, e.g. thermal robustness and increased rate of acidification. The mutations we have identified provide a genetic basis for further investigation of thermal tolerance.
Large rectification magnetoresistance in nonmagnetic Al/Ge/Al heterojunctions
Authors: Zhang Kun , Li Huan-huan , Grünberg Peter , Li Qiang , Ye Sheng-tao , Tian Yu-feng , Yan Shi-shen , Lin Zhao-jun , Kang Shi-shou , Chen Yan-xue , Liu Guo-lei , Mei Liang-mo 
Published: September 2015

AbstractMagnetoresistance and rectification are two fundamental physical properties of heterojunctions and respectively have wide applications in spintronics devices. Being different from the well known various magnetoresistance effects, here we report a brand new large magnetoresistance that can be regarded as rectification magnetoresistance: the application of a pure small sinusoidal alternating-current to the nonmagnetic Al/Ge Schottky heterojunctions can generate a significant direct-current voltage and this rectification voltage strongly varies with the external magnetic field. We find that the rectification magnetoresistance in Al/Ge Schottky heterojunctions is as large as 250% at room temperature, which is greatly enhanced as compared with the conventional magnetoresistance of 70%. The findings of rectification magnetoresistance open the way to the new nonmagnetic Ge-based spintronics devices of large rectification magnetoresistance at ambient temperature under the alternating-current due to the simultaneous implementation of the rectification and magnetoresistance in the same devices.
The brain antigen-specific B cell response correlates with glatiramer acetate responsiveness in relapsing-remitting multiple sclerosis patients
Authors: Rovituso Damiano M. , Duffy Cathrina E. , Schroeter Michael , Kaiser Claudia C. , Kleinschnitz Christoph , Bayas Antonios , Elsner Rebecca , Kuerten Stefanie 
Published: September 2015

AbstractB cells have only recently begun to attract attention in the immunopathology of multiple sclerosis (MS). Suitable markers for the prediction of treatment success with immunomodulatory drugs are still missing. Here we evaluated the B cell response to brain antigens in n = 34 relapsing-remitting MS (RRMS) patients treated with glatiramer acetate (GA) using the enzyme-linked immunospot technique (ELISPOT). Our data demonstrate that patients can be subdivided into responders that show brain-specific B cell reactivity in the blood and patients without this reactivity. Only in patients that classified as B cell responders, there was a significant positive correlation between treatment duration and the time since last relapse in our study. This correlation was GA-specific because it was absent in a control group that consisted of interferon-ß (IFN-β)-treated RRMS patients (n = 23). These data suggest that GA has an effect on brain-reactive B cells in a subset of patients and that only this subset benefits from treatment. The detection of brain-reactive B cells is likely to be a suitable tool to identify drug responders.
Predicting the Lifetime of Dynamic Networks Experiencing Persistent Random Attacks
Authors: Podobnik Boris , Lipic Tomislav , Horvatic Davor , Majdandzic Antonio , Bishop Steven R. , Eugene Stanley H. 
Published: September 2015

AbstractEstimating the critical points at which complex systems abruptly flip from one state to another is one of the remaining challenges in network science. Due to lack of knowledge about the underlying stochastic processes controlling critical transitions, it is widely considered difficult to determine the location of critical points for real-world networks and it is even more difficult to predict the time at which these potentially catastrophic failures occur. We analyse a class of decaying dynamic networks experiencing persistent failures in which the magnitude of the overall failure is quantified by the probability that a potentially permanent internal failure will occur. When the fraction of active neighbours is reduced to a critical threshold, cascading failures can trigger a total network failure. For this class of network we find that the time to network failure, which is equivalent to network lifetime, is inversely dependent upon the magnitude of the failure and logarithmically dependent on the threshold. We analyse how permanent failures affect network robustness using network lifetime as a measure. These findings provide new methodological insight into system dynamics and, in particular, of the dynamic processes of networks. We illustrate the network model by selected examples from biology and social science.
Re-calibration of the magnetic compass in hand-raised European robins (Erithacus rubecula)
Authors: Alert Bianca , Michalik Andreas , Thiele Nadine , Bottesch Michael , Mouritsen Henrik 
Published: September 2015

AbstractMigratory birds can use a variety of environmental cues for orientation. A primary calibration between the celestial and magnetic compasses seems to be fundamental prior to a bird’s first autumn migration. Releasing hand-raised or rescued young birds back into the wild might therefore be a problem because they might not have established a functional orientation system during their first calendar year. Here, we test whether hand-raised European robins that did not develop any functional compass before or during their first autumn migration could relearn to orient if they were exposed to natural celestial cues during the subsequent winter and spring. When tested in the geomagnetic field without access to celestial cues, these birds could orient in their species-specific spring migratory direction. In contrast, control birds that were deprived of any natural celestial cues throughout remained unable to orient. Our experiments suggest that European robins are still capable of establishing a functional orientation system after their first autumn. Although the external reference remains speculative, most likely, natural celestial cues enabled our birds to calibrate their magnetic compass. Our data suggest that avian compass systems are more flexible than previously believed and have implications for the release of hand-reared migratory birds.
An Abiotic Glass-Bead Collector Exhibiting Active Transport
Authors: Goto Youhei , Kanda Masato , Yamamoto Daigo , Shioi Akihisa 
Published: September 2015

AbstractAnimals relocate objects as needed by active motion. Active transport is ubiquitous in living organisms but has been difficult to realize in abiotic systems. Here we show that a self-propelled droplet can gather scattered beads toward one place on a floor and sweep it clean. This is a biomimetic active transport with loadings and unloadings, because the transport was performed by a carrier and the motion of the carrier was maintained by the energy of the chemical reaction. The oil droplet produced fluctuation of the local number density of the beads on the floor, followed by its autocatalytic growth. This mechanism may inspire the technologies based on active transport wherein chemical and physical substances migrate as in living organisms.
Culture’s causes: the next challenge
Authors: Hofstede Gert Jan 
Published: September 2015

Purpose
– The purpose of this paper is to argue that in cross-cultural and strategic management, we must pay attention to the processes creating and maintaining culture. How can everyday interactions give rise to national, “deep” cultures, recognizable across centuries, or organizational cultures, recognizable across decades?

Design/methodology/approach
– This is a conceptual paper using the evidence provided by research about cultural patterns, and using sociological status-power theory to explain the causation of these patterns. Emergence, also called self-organization, is introduced as mechanism connecting individual-level causation with resulting system-level patterns. Cases are used to illustrate points.

Findings
– Simulation gaming and computational social simulation are introduced. These methods allow “growing” a system, thus allowing to experiment with potential interventions and their unanticipated effects.

Research limitations/implications
– This essay could have major implications for research, adding new methods to survey-based and case-based studies, and achieving a new synthesis. Strategic management today almost invariably involves cross-cultural elements. As a result, cross-cultural understanding is now strategically important.

Practical implications
– The suggestions in this essay could lead to new collaborations in the study of culture and organizational processes. Examples include team formation, negotiation, mergers and acquisitions, trans-national collaboration, incentive systems and job interviews.

Social implications
– The suggestions in this essay could contribute to our ability of proactively steering processes in organizations. In particular, they can provide a check to the notion that a control measure necessarily results in its intended effect.

Originality/value
– The synthesis of biological, sociological and cross-cultural psychological viewpoints with design-oriented method, using games or social simulations as research instruments, is original in the field.
Development of a client-based risk management methodology for the early design stage of construction processes
Authors: Albogamy Abdullah , Dawood Nashwan 
Published: September 2015

Purpose
– The risk factors associated with clients have a major impact on the successful delivery of a project from early design to the construction and operation stages. Risk management studies conducted so far have not succeeded in providing an effective risk assessment methodology for clients in analysing and managing the risk factors that cause both project delays and cost overruns. So, the purpose of this paper is to provide a methodology for a client-based risk management model.

Design/methodology/approach
– A conceptual framework is designed by integrating the findings from a literature review and a construction industry survey in the Kingdom of Saudi Arabia. The framework includes the risk identification, risk analysis and mitigation strategy, which are the key components of the model. The model of the framework is developed by integrating the analytical hierarchy process (AHP) and Monte Carlo simulation (MCS) underpinned within an @Risk program.

Findings
– A case study is used to demonstrate the proposed methodology; the results found that the model helps to analyse and quantify the impact of risk factors, and also to assist in taking a suitable risk mitigation strategy, particularly at the early design stage in the construction process.

Practical implications
– The model is applicable to both public and private clients when they need to know the possible project duration in a new construction project, and to take some proactive actions to avoid the adverse effect of client risk factors at the early stage of the project.

Originality/value
– The model is expected to help in understanding the nature, and analysing the influence, of client risk factors that cause project delays and cost overruns. The development of the methodology for managing the client-based risk in construction processes at the early design stage is the key value of the study.
The impact of brain drain in underserved countries: implementing a global ethical leadership approach
Authors: Grenier Marie-Lyne 
Published: September 2015

Purpose
– Health care worker migration from underserved nations to developed nations, also known as the “brain drain” effect, is a leading cause of worldwide health inequalities. The purpose of this paper is to identify the factors which have and continue to contribute to “brain drain,” investigate the human consequences of health care worker migration, and explore the ways in which a global ethical leadership approach could be used to help address the issue of “brain drain” and its resulting deleterious effects on global health equality.

Design/methodology/approach
– An argument is made supporting the need for a global leadership approach that is centered on the enforcement of ethical international health care worker recruitment policies and collaborative endeavors between wealthy and underserved nations to help improve the working conditions of health care workers worldwide.

Findings
– The successful use of ethical leadership approaches in addressing and reversing the “brain drain” effect has been documented in Thailand and Ireland. These case examples could be used as templates for future legislative action on a global scale.

Originality/value
– This piece highlights the urgent need for a global ethical leadership approach to help address the issue of “brain drain” in underserved nations and provides concrete strategies to help guide legislative decision making.
Understanding establishment mode choice of foreign manufacturing firms in Ghana
Authors: Dadzie Samuel Ato , Owusu Richard Afriyie 
Published: September 2015

Purpose– The purpose of this paper is to analyse the foreign direct investment (FDI) strategies of manufacturing firms in Ghana using the eclectic model in order to understand how ownership, location and internalization factors impact FDI to developing countries like Ghana.Design/methodology/approach– The authors use a quantitative methodology in order to statistically explore the relationships between dependent and independent variables. The data comes from a sample of 75 multinational enterprises that invested in the manufacturing sector between 1994 and 2008.Findings– The results reveal that large firm size, extensive international experience and large market size lead to the choice of acquisition mode of entry, while high cultural distance, high country risk, high proprietary assets and incentives lead to the choice of greenfield mode in the context of Ghana.Research limitations/implications– The results imply that the different economic, business and legal (locational) conditions of developing countries create different FDI strategies and paths of companies compared to developed markets.Practical implications– Policy makers in developing countries should make efforts to improve market size, the institutional and regulatory environment, as well as the availability of human capital in order to attract FDI.Originality/value– FDI studies have mainly analysed establishment mode strategies of firms in advanced markets. There is an increasing amount of research on FDI in emerging markets but very little on developing countries and African markets. Therefore, this study enables the authors to develop implications for existing theory and generate practical implications for firms and policy makers related to African and developing country markets.
Consumers’ attitude towards social media advertising and their behavioural response
Authors: Boateng Henry , Okoe Abednego Feehi 
Published: September 2015

Purpose– The purpose of this study is to examine the relationship between consumers’ attitude toward social media advertising and their behavioural response and the moderating effect of corporate reputation in this relationship. Social media advertising is gradually gaining grounds among practitioners and researchers.Design/methodology/approach– Survey design was used and the respondents totaled 441. They were selected using convenience sampling technique. Questionnaires were used to collect the data and analyzed using hierarchical regression.Findings– Findings indicate that there is a significant relationship between consumers’ attitude toward social media advertising and their behavioural responses. Again, it was noted that corporate reputation moderates this relationship.Research limitations/implications– This study relied on convenience sampling and a cross-sectional survey design, which makes it difficult to generalize the findings and account for changes that occurred in the attitude of consumers.Originality/value– This study contributes to the understanding of the moderating role of corporate reputation in consumers’ attitude toward social media advertising.