bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research
Authors: De Jager Phillip L , Ma Yiyi , McCabe Cristin , Xu Jishu , Vardarajan Badri N. , Felsky Daniel , Klein Hans-Ulrich , White Charles C. , Peters Mette A. , Lodgson Ben , Nejad Parham , Tang Anna , Mangravite Lara M. , Yu Lei , Gaiteri Chris , Mostafavi Sara , Schneider Julie A. , Bennett David A. 
Published: January 2018

AbstractWe initiated the systematic profiling of the dorsolateral prefrontal cortex obtained from a subset of autopsied individuals enrolled in the Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP), which are jointly designed and belong to a very few prospective studies of aging and dementia with detailed, longitudinal cognitive phenotyping during life and a quantitative, structured neuropathologic examination after death for >3,322 subjects. Here, we outline the first generation of data including genome-wide genotypes (n=2,090), whole genome sequencing (n=1,179), DNA methylation (n=740), chromatin immunoprecipitation with sequencing using an anti-Histone 3 Lysine 9 acetylation (H3K9Ac) antibody (n=712), RNA sequencing (n=638), and miRNA profile (n=702). Generation of other omic data including ATACseq, proteomic and metabolomics profiles is ongoing. Thanks to its prospective design and recruitment of older, non-demented individuals, these data can be repurposed to investigate a large number of syndromic and quantitative neuroscience phenotypes. The many subjects that are cognitively non-impaired at death also offer insights into the biology of the human brain in older non-impaired individuals.
Whole-genome resequencing and pan-transcriptome reconstruction highlight the impact of genomic structural variation on secondary metabolism gene clusters in the grapevine Esca pathogenPhaeoacremonium minimum
Authors: Massonnet Mélanie , Morales-Cruz Abraham , Minio Andrea , Figueroa-Balderas Rosa , Lawrence Daniel P. , Travadon Renaud , Rolshausen Philippe E. , Baumgartner Kendra , Cantu Dario 
Published: January 2018

ABSTRACTThe Ascomycete fungusPhaeoacremonium minimumis one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence amongPm. minimumisolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference ofPm. minimumcomprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included thePm. minimumpan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.
Polygenic scores for UK Biobank scale data
Authors: Mak Timothy Shin Heng , Porsch Robert Milan , Choi Shing Wan , Sham Pak Chung 
Published: January 2018

AbstractPolygenic scores (PGS) are estimated scores representing the genetic tendency of an individual for a disease or trait and have become an indispensible tool in a variety of analyses. Typically they are linear combination of the genotypes of a large number of SNPs, with the weights calculated from an external source, such as summary statistics from large meta-analyses. Recently cohorts with genetic data have become very large, such that it would be a waste if the raw data were not made use of in constructing PGS. Making use of raw data in calculating PGS, however, presents us with problems of overfitting. Here we discuss the essence of overfitting as applied in PGS calculations and highlight the difference between overfitting due to the overlap between the target and the discovery data (OTD), and overfitting due to the overlap between the target the the validation data (OTV). We propose two methods — cross prediction and split validation — to overcome OTD and OTV respectively. Using these two methods, PGS can be calculated using raw data without overfitting. We show that PGSs thus calculated have better predictive power than those using summary statistics alone for six phenotypes in the UK Biobank data.
Ethylene mitigates waterlogging stress by regulating glutathione biosynthesis-related transcripts in soybeans
Authors: Kim Yoonha , Seo Chang-Woo , Khan Abdul Latif , Mun Bong-Gyu , Shahzad Raheem , Ko Jung-Woo , Yun Byung-Wook , Lee In-Jung 
Published: January 2018

AbstractWaterlogging stress is a restrictive factors in soybean productivity worldwide. Plants utilize various physio-chemical changes to mitigate waterlogging stress. In current study, the regulatory roles of seven kinds of plant growth regulators, including abscisic acid (ABA), ethylene (ethephon, ETP), gibberellins (GA4), indole-3-acetic acid (IAA), kinetine (KT), jasmonic acid (JA) and salicylic acid (SA), were determined for soybeans under waterlogging conditions. Based on the results, the donor source of ethylene was selected and its role was further examined regarding physiochemical alteration and glutathione biosynthesis-related transcripts through application of exogenous ETP. ETP application mitigated waterlogging stress and significantly improved the efficiency of photosynthesis and increased bioactive GA4 contents compared to that of untreated plants. Element and amino acid contents among the treatments were significantly different. Total elements and amino acid contents were increased in 100 μM ETP-treated soybean plants. ETP application induced adventitious root initiation, improved root surface area, and significantly increased glutathione transferases expression and glutathione relative to that of non-ETP treated soybean plants. Finally, 100 μM-ETP application induced up-regulated protein content and glutathione s-transferase DHAR2 as compared to that of soybeans under waterlogging-conditions only. ETP could induce various biochemical and transcriptional modulations that strengthen plant growth and mitigate waterlogging stress.HighlightEthylene application to soybean plants after waterlogging up-regulates glutathione transferase genes. Higher glutathione activity, as well as increased glutathione s-transferase DHAR2 protein content was induced to scavenge reactive oxygen species.
The fitness landscape of the codon space across environments
Authors: Fragata Inès , Matuszewski Sebastian , Schmitz Mark A. , Bataillon Thomas , Jensen Jeffrey D. , Bank Claudia 
Published: January 2018

AbstractFitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitness effects of synonymous mutations and their potential impact on adaptation on a fitness landscape, we use a new software based on Bayesian Monte Carlo Markov Chain methods and reestimate selection coefficients of all possible codon mutations across 9 amino-acid positions inSaccharomyces cerevisiaeHsp90 across 6 environments. We quantify the distribution of fitness effects of synonymous mutations and show that it is dominated by many mutations of small or no effect and few mutations of larger effect. We then compare the shape of the codon fitness landscape across amino-acid positions and environments, and quantify how the consideration of synonymous fitness effects changes the evolutionary dynamics on these fitness landscapes. Together these results highlight a possible role of synonymous mutations in adaptation and indicate the potential mis-inference when they are neglected in fitness landscape studies.
Feedback control of neurogenesis by tissue packing
Authors: Hiscock Tom W. , Miesfeld Joel B. , Mosaliganti Kishore R. , Link Brian A. , Megason Sean G. 
Published: January 2018

AbstractBalancing the rate of differentiation and proliferation in developing tissues is essential to produce organs of robust size and composition. Whilst many molecular regulators have been established, how these connect to physical and geometrical aspects of tissue architecture is poorly understood. Here, using high-resolution timelapse imaging, we find that dense tissue packing and complex cell geometries play a significant role in regulating differentiation rate in the zebrafish neural tube. Specifically, in regions of high cell density, progenitors are physically pushed away from the apical surface, which, in a Notch-dependent manner, leads to their differentiation. Using simulations we show that this naturally performs negative feedback control on cell number. Our results suggest a model whereby differentiation rate is carefully tuned to correct fluctuations in cell number, originating from variable cell cycle progression and inherently probabilistic differentiation programs.
Chiral cilia orientation in the left-right organizer
Authors: Ferreira Rita R. , Pakula Guillaume , Klaeyle Lhéanna , Fukui Hajime , Vilfan Andrej , Supatto Willy , Vermot Julien 
Published: January 2018

AbstractChirality is a property of asymmetry between an object and its mirror image. Most biomolecules and cells are intrinsically chiral. Whether cellular chirality can be transferred to asymmetry at the tissue scale remains an unresolved issue. This question is particularly relevant in the left-right organizer (LRO), where cilia motility and chiral flow are thought to be the main drivers of left-right axis symmetry breaking. Here, we built a quantitative approach based on live imaging to set apart the contributions of various pathways to the spatial orientation of cilia in the Kupffer’s vesicle (KV, zebrafish LRO). We found that cilia populating the zebrafish LRO display an asymmetric orientation between the right and left side of the LRO. Cilia orientations, therefore, give the KV cells a sense of chirality which is different from the chirality of cilia rotation. Surprisingly, we found this asymmetry does not depend on the left-right signalling pathway or flow. Furthermore, we show the establishment of the chirality is dynamic and depends on planar cell polarity. Together, this work identifies a different type of asymmetry in the LRO and sheds light on the complexity of chirality genesis in developing tissues.
ITU cost model and methodology to assist national regulatory authorities to engage with international mobile roaming
Authors: Forge Simon , Srivastava Lara 
Published: January 2018

Purpose
Tariffs for international mobile roaming (IMR) are often viewed by governments as an additional tax on international trade and on tourism. IMR customer bills may appear to be arbitrary and sometimes excessive. The purpose of this paper is therefore to set out a pragmatic approach to assessing international charges for mobile roaming, making use of a realistic cost model of the international roaming process and its cost elements, at a level that is useful to regulatory authorities and operators.

Design/methodology/approach
The discussion presented is based on industry practices for handling voice calls and data sessions with the mobile network operators (MNOs) business model, based on industry sources. The basic mechanisms use two common constructs from business analysis – business processes and use-cases – to provide a simplified form of activity-based costing. This provides a model suitable for national regulatory authorities to move towards cost-based IMR tariffs.

Findings
Using a perspective on costs based on a bottom-up survey procedure for elucidating the key information, the paper presents the cost elements for the various IMR network components and business processes, with an approach suitable for analysing both wholesale and retail pricing.

Research limitations/implications
The method is specifically designed to overcome the key problem of such approaches, the limitations set by differences in network technologies, network topology, operational scale and the engineering, as well as MNO business model and accounting practices, which otherwise would preclude the method presented here from being vendor neutral.

Practical implications
Vendor and network engineering neutrality implies the approach can be used to compare different MNOs in terms of the validity of their IMR charges and whether they are cost based.

Social implications
Impacts on society of so-called “bill-shock” have become quite common, increasingly for data sessions. The cost model presented here was developed with the intention of improving the accountability and transparency of the mobile roaming market. It thus assists in the introduction of cost-based tariffs over an economic region, such the European Union.

Originality/value
The paper examines the practical implications of building large-scale cost models for assessing the real IMR costs, a modelling exercise that has not been seen elsewhere in terms of its approach and neutrality as to MNO structure and assets.
Spot the difference: examining facial characteristics that enhance spokesperson effectiveness
Authors: Ilicic Jasmina , Baxter Stacey M. , Kulczynski Alicia 
Published: January 2018

Purpose
This research aims to examine the effect of spokesperson facial symmetry on advertisement attitude, brand attitude and purchase intention and the mediating role of source authenticity on attitudinal and behavioral judgments.

Design/methodology/approach
Two studies were undertaken. Study 1 examined the effect of facial symmetry on source authenticity and endorsement effectiveness. Study 2 investigated the influence of the authentic facial cues of freckles and moles on source authenticity and advertisement attitude, brand attitude and purchase intention.

Findings
Findings indicate that source authenticity is the mechanism that explains attitudinal and behavioral judgments toward advertisements featuring asymmetrical spokespeople. The phenomenon observed is due to a proposed source authenticity overgeneralization effect, whereby spokespeople with asymmetrical faces are perceived as more genuine and real which, subsequently, results in more positive attitude toward the advertisement, attitude toward the brand and greater purchase intention than advertisements featuring spokespeople with symmetrical faces. The addition of authentic (biological) facial cues (i.e. freckles and moles) on spokespeople with a symmetrical facial structure, however, can heighten perceptions of source authenticity and the manifestation of the source authenticity overgeneralization effect.

Research limitations/implications
This research has implications for marketing managers in the selection and depiction of spokespeople in their advertisements. However, this research is limited, as it only examines the facial feature characteristics of symmetry, freckles, and moles.

Originality/value
This research shows that an asymmetrical facial structure can positively influence source, attitudinal and behavioral judgments. This research also identifies that although symmetrical facial structures dilute source- and endorsement-based judgments, the addition of authentic facial cues, freckles and moles, can reverse the negative effects and enhance perceptions of source authenticity, attitude toward the advertisement, attitude toward the brand and purchase intentions.
Cruise tourism: a hedonic pricing approach
Authors: Espinet-Rius Josep Maria , Fluvià-Font Modest , Rigall-Torrent Ricard , Oliveras-Corominas Anna 
Published: January 2018

Purpose
The purpose of this paper is to examine the effect on price of different cruise industry characteristics from the point of view of actual prices. The analysis is carried out from the supply side but taking into account the real prices paid by customers.

Design/methodology/approach
This paper uses the hedonic price methodology. To develop this research, a database of more than 36,000 prices paid by cruise passengers and different characteristics of ships in 2013 was built. To obtain the results, ten models have been developed with significant adjusted R2 of between 0.85 and 0.93 making the models and results robust.

Findings
The results show that the main attributes affecting prices are the number of nights of the itinerary, the departure date, the number of days before departure the booking is made, the accommodation type and some facilities, such as casinos, cinemas and swimming pools. The results also yield a ranking of ship companies based on price and quality dimensions. Finally, the authors suggest some implications for management and new research.

Originality/value
This paper offers a new approach in the academic literature of the cruise industry in two respects. First, in its use of a broad database of actual prices paid by passengers – more than 36,000 observations. Second, in the application of the hedonic pricing methodology, widely used in the tourism sector (see the Methodology and Database section) but until now not in the cruising segment.
Entrepreneurship education pedagogy: teacher-student-centred paradox
Authors: Ismail Annafatmawaty B.T. , Sawang Sukanlaya , Zolin Roxanne 
Published: January 2018

PurposeThe purpose of this paper is to answer the research question: “Do different pedagogies used in teaching entrepreneurship education influence individual skill development, which then in turn translates into a likelihood of entrepreneurial implementation intention?”Design/methodology/approachThe number of total participants for the quasi-experiment was 308 undergraduate students in Malaysia, in which pre- and post-test (n=203) and control (n=105) groups are included. Students who enroled in the entrepreneurship course were randomly allocated into a class employing teacher-centred pedagogy or student-centred pedagogy. Learning outcomes are measured by objective and subjective measures.FindingsBoth pedagogical approaches had a positive effect on the development of the learning outcomes. However, the students who learned using the teacher-centred approach statistically developed a higher level of objective and subjective learning outcomes compared to the students who learned using the student-centred approach. The findings also suggest that the relationship between entrepreneurship education and entrepreneurial intention mediates by learned skills.Originality/valueThe quasi-experimental design greatly improves the ability to make accurate claims about the impact of entrepreneurial education on entrepreneurship-related outcomes. Further, the study uses the implementation intention strategy in measuring the entrepreneurial intention. Thus, the study strongly supports for the view that implementation intention improves predictive validity of the behavioural intention within the framework of theory of planned behaviour by setting out in advance when, where, and how the goal will be achieved.
The VUCA approach as a solution concept to corporate foresight challenges and global technological disruption
Authors: Kaivo-oja Jari Roy Lee , Lauraeus Iris Theresa 
Published: January 2018

Purpose
Under current market conditions of corporate foresight, turbulence is a key element of the business landscape. Turbulence can be summarised using the trendy managerial acronym “VUCA”: volatility, uncertainty, complexity and ambiguity. This paper aims to combine, for the first time, scientific discussion of technological disruption with the VUCA approach. Gartner Hype Cycle is used as a case example of technological turbulence and “vucability”.

Design/methodology/approach
First, the authors present the key concepts of technological disruption and radical innovation. Both these concepts are highly relevant for modern corporate foresight. Second, the authors discuss the key elements of current technological transformation and summarise it to create a bigger picture. Third, the authors link this discussion to the VUCA approach. Fourth, the authors present the new corporate foresight framework, which is highly relevant for corporations and takes current technological transformation more seriously than previous proposals, which expect more stable business and a technological landscape.

Findings
Key issues in modern VUCA management are agility (response to volatility), information and knowledge management (response to uncertainty), restructuring (response to complexity) and experimentation (response to ambiguity). Useful foresight tools are challenging tools, decision-making tools, aligning tools, learning tools and the ability to combine these management tools in the practices of corporate foresight and management systems. The VUCA approach is a key solution concept to technological disruption.

Practical implications
The authors present the new corporate foresight framework and management tool based on foresight, which help leaders to manage VUCA – especially under the conditions of hyper-competition and technological disruption.

Originality/value
Corporate leaders should reinvent the strategic planning framework and adjust it to the VUCA conditions and simply be more strategic. Traps and typical failures of foresight are adopting it too early, giving up too soon, adapting too late and hanging on too long. In particular, technological transformation with disruptive technologies is changing and challenging many basic assumptions of business management and strategic planning. Our comparative analysis with Gartner Hype Cycle (fast technological changes from 2008 to 2016) verifies this important aspect of technological disruption.