bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome
Authors: Pincus David , Anandhakumar Jayamani , Thiru Prathapan , Guertin Michael J. , Erkine Alexander M. , Gross David S. 
Published: April 2018

AbstractHeat Shock Factor 1 (Hsf1) is the master transcriptional regulator of molecular chaperones and binds to the same cis-acting element - Heat Shock Element (HSE) - across the eukaryotic lineage. In budding yeast, Hsf1 drives transcription of ~20 genes essential to maintain proteostasis under basal conditions, yet its specific targets and extent of inducible binding during heat shock remain unclear. Here we combine Hsf1 ChIP-seq, nascent RNA-seq and Hsf1 nuclear depletion to quantify Hsf1 binding and transcription across the yeast genome. Hsf1 binds 74 loci during acute heat shock, 46 of which are linked to genes with strong Hsf1-dependent transcription. Most of these targets show detectable Hsf1 binding under basal conditions, but basal occupancy and heat shock-inducible binding both vary over two orders of magnitude. Notably, Hsf1’s induced DNA binding leads to a disproportionate (up to 50-fold) increase in nascent transcription. While variation in basal Hsf1 occupancy poorly correlates with the strength of the HSE, promoters with high basal Hsf1 occupancy have nucleosome-depleted regions due to the presence of ‘pioneer’ factors. Such accessible chromatin may be critical for Hsf1 occupancy of its genomic sites as the activator is incapable of binding HSEs embedded within a stable nucleosome in vitro. In response to heat shock, however, Hsf1 is able to gain access to nucleosomal sites and promotes chromatin remodeling with the RSC complex playing a key role. We propose that the interplay between nucleosome occupancy, HSE strength and active Hsf1 levels allows cells to precisely tune expression of the proteostasis network.
Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads
Authors: Nguyen Huy , Roy Jagoree , Harink Björn , Damle Nikhil , Baxter Brian , Brower Kara , Kortemme Tanja , Thorn Kurt , Cyert Martha , Fordyce Polly 
Published: April 2018

AbstractTransient, regulated binding of globular protein domains to Short Linear Motifs (SLiMs) in disordered regions of other proteins drives cellular signaling. Mapping the energy landscapes of these interactions is essential for deciphering and therapeutically perturbing signaling networks, but is challenging due to their weak affinities. We present a powerful technology, MRBLE-pep, that simultaneously quantifies protein binding to a library of peptides directly synthesized on beads containing unique spectral codes. Using computational modeling and MRBLE-pep, we systematically probe binding of calcineurin (CN), a conserved protein phosphatase essential for the immune response and target of immunosuppressants, to the PxIxIT SLiM. We establish that flanking residues and post- translational modifications critically contribute to PxIxIT-CN affinity, and discover CN-inhibitory peptides with unprecedented affinity and therapeutic potential. The quantitative measurements provided by this approach will improve computational modeling efforts, elucidate a broad range of weak protein-SLiM interactions, and revolutionize our understanding of signaling networks.
The role of maternal pioneer factors in predefining first zygotic responses to inductive signals
Authors: Gentsch George E. , Spruce Thomas , Owens Nick D. L. , Smith James C. 
Published: April 2018

ABSTRACTEmbryonic development yields many different cell types in response to just a few families of inductive signals. The property of a signal-receiving cell that determines how it responds to such signals, including the activation of cell type-specific genes, is known as its competence. Here, we show how maternal factors modify chromatin to specify initial competence in the frogXenopus tropicalis. We identified the earliest engaged regulatory DNA sequences, and inferred from them critical activators of the zygotic genome. Of these, we showed that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox3 predefines competence for germ layer formation by extensively remodeling compacted chromatin before the onset of signaling. The remodeling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work identifies significant developmental principles that inform our understanding of how pluripotent stem cells interpret inductive signals.
A New Approach to Symmetric Registration of Longitudinal Structural MRI of the Human Brain
Authors: Ardekani Babak A. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2018

AbstractThis technical report presents the Automatic Temporal Registration Algorithm (ATRA) for symmetric rigid-body affine registration of longitudinal T1-weighted three-dimensional magnetic resonance imaging (MRI) scans of the human brain. This is a fundamental processing step in computational neuroimaging. The notion of leave-one-out consistent (LOOC) landmarks with respect to a supervised landmark detection algorithm is introduced. An automatic algorithm is presented for identification of LOOC landmarks on MRI scans. Using this technique, multiple sets of LOOC landmarks (around 150) are identified on each of the volumes being registered. Then, a Generalized Orthogonal Procrustes Analysis of the identified landmarks is used to find a rigid-body transformation of each volume into a common space where the transformed volumes are precisely aligned. In addition, a new approach is introduced for quantitative assessment of registration accuracy in the absence of a gold standard. Qualitative and quantitative evaluations of ATRA registration accuracy are performed using 2012 volumes from 503 subjects (4 longitudinal volumes/subject) from the Alzheimer’s Disease Neuroimaging Initiative database, and on a further 120 volumes acquired from 3 normal subjects (40 longitudinal volumes/subject). The algorithm is symmetric, in the sense that any permutation of the input volumes does not change the resulting transformation matrices, and unbiased, in the sense that all volumes undergo one and only one interpolation operation, which precisely aligns them in a common space. There is no interpolation bias and no reference volume. All volumes are treated exactly the same. The algorithm is fast and highly accurate. The software is publicly available.
Deciphering the Dynamics of Interlocked Feedback Loops in a Model of the Mammalian Circadian Clock
Authors: Battogtokh Dorjsuren , Tyson John J. 
Published: April 2018

AbstractMathematical models of fundamental biological processes play an important role in consolidating theory and experiments, especially if they are systematically developed, thoroughly characterized, and well tested by experimental data. In this work, we report a detailed bifurcation analysis of a mathematical model of the mammalian circadian clock network developed by Relogio et al. [16], noteworthy for its consistency with available data. Using one- and two-parameter bifurcation diagrams, we explore how oscillations in the model depend on the expression levels of its constituent genes and the activities of their encoded proteins. These bifurcation diagrams allow us to decipher the dynamics of interlocked feedback loops, by parametric variation of genes and proteins in the model. Among other results, we find that REV-ERB, a member of a subfamily of orphan nuclear receptors, plays a critical role in the intertwined dynamics of Relogio’s model. The bifurcation diagrams reported here can be used for predicting how the core-clock network responds—in terms of period, amplitude and phases of oscillations—to different perturbations.
RAPTOR Controls Developmental Growth Transitions by Altering the Hormonal and Metabolic Balance
Authors: Salem Mohamed A. , Li Yan , Bajdzienko Krzysztof , Fisahn Joachim , Watanabe Mutsumi , Hoefgen Rainer , Schöttler Mark Aurel , Giavalisco Patrick 
Published: April 2018

Abstract
Vegetative growth requires the systemic coordination of numerous cellular processes, which are controlled by regulatory proteins that monitor extracellular and intracellular cues and translate them into growth decisions. In eukaryotes, one of the central factors regulating growth is the serine/threonine protein kinase Target of Rapamycin (TOR), which forms complexes with regulatory proteins. To understand the function of one such regulatory protein, Regulatory-Associated Protein of TOR 1B (RAPTOR1B), in plants, we analyzed the effect of raptor1b mutations on growth and physiology in Arabidopsis (Arabidopsis thaliana) by detailed phenotyping, metabolomic, lipidomic, and proteomic analyses. Mutation of RAPTOR1B resulted in a strong reduction of TOR kinase activity, leading to massive changes in central carbon and nitrogen metabolism, accumulation of excess starch, and induction of autophagy. These shifts led to a significant reduction of plant growth that occurred nonlinearly during developmental stage transitions. This phenotype was accompanied by changes in cell morphology and tissue anatomy. In contrast to previous studies in rice (Oryza sativa), we found that the Arabidopsis raptor1b mutation did not affect chloroplast development or photosynthetic electron transport efficiency; however, it resulted in decreased CO2 assimilation rate and increased stomatal conductance. The raptor1b mutants also had reduced abscisic acid levels. Surprisingly, abscisic acid feeding experiments resulted in partial complementation of the growth phenotypes, indicating the tight interaction between TOR function and hormone synthesis and signaling in plants.
The Pentatricopeptide Repeat Protein SOT5/EMB2279 Is Required for Plastid rpl2 and trnK Intron Splicing
Authors: Huang Weihua , Zhu Yajuan , Wu Wenjuan , Li Xuan , Zhang Delin , Yin Ping , Huang Jirong 
Published: April 2018

Abstract
Chloroplast biogenesis and development are highly complex processes requiring interaction between plastid and nuclear genomic products. Using a high-throughput screen for chloroplast biogenesis suppressors in Arabidopsis (Arabidopsis thaliana), we identified a suppressor of thf1 (sot5) that displays virescent and serrated leaves. Further characterization revealed that sot5 mutants are defective in leaf adaxial and abaxial polarity and act as enhancers of asymmetric leaves2. Map-based cloning identified SOT5 as a gene previously named EMB2279 that encodes a plastid-targeted pentatricopeptide repeat (PPR) protein with 11 PPR motifs. A G-to-A mutation in sot5 leads to a significant decrease in splicing efficiency, generating two additional mRNA variants. As reported previously, the sot5 null mutation is embryo lethal. SOT5 is predicted to bind to specific RNA sequences found in plastid rpl2 and trnK genes, and we found decreased splicing efficiency of the rpl2 and trnK genes in sot5 mutants. Together, our results reveal that the PPR protein SOT5/EMB2279 is required for intron splicing of plastid rpl2 and trnK, providing insights into the role of plastid translation in the coupled development between chloroplasts and leaves.
“One foot in industry, the other in academia”
Authors: Galan Nataliya 
Published: April 2018

PurposeThe purpose of this paper is to examine professional service firms’ (PSFs) motives and benefits related to their engagement in knowledge transfer interactions with universities via their employees also acting as adjunct professors (APs).Design/methodology/approachThe study adopts a qualitative approach relying mainly on data collected via semi-structured interviews with both top managers and APs employed by five engineering consultancies operating in Sweden.FindingsThe findings suggest that, while seeking stability is the major determinant of engagement in relations with universities via APs, PSFs highpoint the significance of reciprocity and legitimacy motives. The most substantial benefits appear to be related to firms’ access to academic research, core competencies and human resource development as well as marketing outcomes. Benefits are found to be dynamic in character with higher-order benefits being generated by low-order over time.Research limitations/implicationsThe findings rely on a small sample of PSFs and should be verified by future research with larger samples of PSFs operating in a broader range of industries and national contexts.Practical implicationsThe study results may be of interest to managers of both firms and universities interested in establishing, formalising or broadening university-industry interactions.Originality/valueThe study advances the current knowledge on the rationales of service firms engaged in various university-industry knowledge transfer interactions by making empirical and conceptual contributions to the understanding of adjunct professorship as a particular form of such interactions.
Analyzing and forecasting the Chinese term structure of interest rates using functional principal component analysis
Authors: Feng Pan , Qian Junhui 
Published: April 2018

Purpose
The purpose of this paper is to analyze and forecast the Chinese term structure of interest rates using functional principal component analysis (FPCA).

Design/methodology/approach
The authors propose an FPCA-K model using FPCA. The forecasting of the yield curve is based on modeling functional principal component (FPC) scores as standard scalar time series models. The authors evaluate the out-of-sample forecast performance using the root mean square and mean absolute errors.

Findings
Monthly yield data from January 2002 to December 2016 are used in this paper. The authors find that in the full sample, the first two FPCs account for 98.68 percent of the total variation in the yield curve. The authors then construct an FPCA-K model using the leading principal components. The authors find that the FPCA-K model compares favorably with the functional signal plus noise model, the dynamic Nelson-Siegel models and the random walk model in the out-of-sample forecasting.

Practical implications
The authors propose a functional approach to analyzing and forecasting the yield curve, which effectively utilizes the smoothness assumption and conveniently addresses the missing-data issue.

Originality/value
To the best knowledge, the authors are the first to use FPCA in the modeling and forecasting of yield curves.
Re-thinking and re-operationalizing product innovation capability
Authors: Sharma Sumeet Om , Martin Angela 
Published: April 2018

PurposeThis paper aims to enhance the understanding of the essence of product innovation capability (PIC) as a dynamic capability by systematically assessing its conceptualization and construct validity. The paper answers the call by numerous researchers to undertake research efforts to better understand and operationalize dynamic capability constructs.Design/methodology/approachA priori and scholarly contentions based on complementarities between the tenets of three prominent frameworks (Dynamic Capability View, Process Management and Organizational Ambidexterity) were utilized for conducting a theoretical triangulation, as presented in the paper. Established approaches to explication and measurement of multi-dimensional latent constructs were used for guiding this paper.FindingsThis paper enhances the conceptualization of dynamic capabilities and identifies a lacuna in frequently adopted PIC operationalization approaches that is pertinent to other dynamic capabilities. It presents substantive and specific prescriptions for enabling the development of superior capability (both dynamic and operational) measurement models in empirical research.Research limitations/implicationsThe diverse implications for research and practice are discussed in the paper alongside suggestions for future research.Originality/valueThis paper guides future theoretical and empirical research by reviewing the conception and validity of PIC. It presents a comprehensive conception of dynamic capabilities by extending the dynamic capability definition to address the identified problems. The arguments presented have wide-ranging applications and broad generalizability across multiple research fields.
Gamification of health education
Authors: Kostenius Catrine , Hallberg Josef , Lindqvist Anna-Karin 
Published: April 2018

PurposeThe use of modern technology has many challenges and risks. However, by collaborating with schoolchildren, ideas to effectively promote health and learning in school can be identified. The purpose of this paper is to examine how a participatory approach can deepen the understanding of how schoolchildren relate to and use gamification as a tool to promote physical activity and learning.Design/methodology/approachInspired by the concept and process of empowerment and child participation, the methodological focus of this study was on consulting schoolchildren. During a two-month period, 18 schoolchildren (10-12 years old) participated in workshops to create game ideas that would motivate them to be physically active and learn in school.FindingsThe phenomenological analysis resulted in one main theme, “Playing games for fun to be the best I can be.” This consisted of four themes with two sub-themes each. The findings offer insights on how to increase physical activity and health education opportunities using serious games in school.Originality/valueThe knowledge gained provides gamification concepts and combinations of different technological applications to increase health and learning, as well as motivational aspects suggested by the schoolchildren. The findings are discussed with health promotion and health education in mind.
A computational design method for bio-mimicked horizontal axis tidal turbines
Authors: Kulkarni Siddharth Suhas , Chapman Craig , Shah Hanifa , Edwards David John 
Published: April 2018

Purpose
The purpose of this paper is to conduct a comparative analysis between a straight blade (SB) and a curved caudal-fin tidal turbine blade (CB) and to examine the aspects relating to geometry, turbulence modelling, non-dimensional forces lift and power coefficients.

Design/methodology/approach
The comparison utilises results obtained from a default horizontal axis tidal turbine with turbine models available from the literature. A computational design method was then developed and implemented for “horizontal axis tidal turbine blade”. Computational fluid dynamics (CFD) results for the blade design are presented in terms of lift coefficient distribution at mid-height blades, power coefficients and blade surface pressure distributions. Moving the CB back towards the SB ensures that the total blade height stays constant for all geometries. A 3D mesh independency study of a “straight blade horizontal axis tidal turbine blade” modelled using CFD was carried out. The grid convergence study was produced by employing two turbulence models, the standard k-ε model and shear stress transport (SST) in ANSYS CFX. Three parameters were investigated: mesh resolution, turbulence model, and power coefficient in the initial CFD, analysis.

Findings
It was found that the mesh resolution and the turbulence model affect the power coefficient results. The power coefficients obtained from the standard k-ε model are 15 to 20 per cent lower than the accuracy of the SST model. Further analysis was performed on both the designed blades using ANSYS CFX and SST turbulence model. The variation in pressure distributions yields to the varying lift coefficient distribution across blade spans. The lift coefficient reached its peak between 0.75 and 0.8 of the blade span where the total lift accelerates with increasing pressure before drastically dropping down at 0.9 onwards due to the escalating rotational velocity of the blades.

Originality/value
The work presents a computational design methodological approach that is entirely original. While this numerical method has proven to be accurate and robust for many traditional tidal turbines, it has now been verified further for CB tidal turbines.
Urban carbon dioxide equivalent (CO2e) accounting based on the GPC framework
Authors: Jia Junsong , Gong Zhihai , Chen Chundi , Jian Huiyong , Xie Dongming 
Published: April 2018

Purpose
This paper aims to provide a typical example of accounting for the carbon dioxide equivalent (CO2e) in underdeveloped cities, especially for the Poyang Lake area in China. The accounting can increase public understanding and trust in climate mitigation strategies by showing more detailed data.

Design/methodology/approach
The paper uses the “Global Protocol for Community-scale greenhouse gas emission inventories (GPC)” method, a worldwide comparable framework for calculating urban CO2e emission (CE). The empirical case is an underdeveloped city, Nanchang, in China.

Findings
The results show the total CE of Nanchang, containing the electricity CE of Scope 2, grew rapidly from 12.49 Mt in 1994 to 55.00 Mt in 2014, with the only recession caused by the global financial crisis in 2008. The biggest three contributors were industrial energy consumption, transportation and industrial processes, which contributed 44.71-72.06, 4.10-25.07 and 9.07-22.28 per cent, respectively, to the total CE. Almost always, more than 74.41 per cent of Nanchang’s CE was related to coal. When considering only the CEs from coal, oil and gas, these CEs per unit area of Nanchang were always greater than those of China and the world. Similarly, these CEs per gross domestic product of Nanchang were always bigger than those of the world. Thus, based on these conclusions, some specific countermeasures were recommended.

Originality/value
This paper argues that the CO2e accounting of underdeveloped cities by using the GPC framework should be promoted when designing climate mitigation policies. They can provide more scientific data to justify related countermeasures.
Climate variability, perceptions of pastoralists and their adaptation strategies
Authors: Ayal Desalegn Yayeh , Radeny Maren , Desta Solomon , Gebru Getachew 
Published: April 2018

Purpose
Climate variability and extremes adversely affect the livestock sector directly and indirectly by aggravating the prevalence of livestock diseases, distorting production system and the sector profitability. This paper aims to examine climate variability and its impact on livestock system and livestock disease among pastoralists in Borana, Southern Ethiopia.

Design/methodology/approach
Data were collected through a combination of quantitative and qualitative methods using household questionnaire, field observations, focus group discussions and key informant interviews. Areal grid dikadal rainfall and temperatures data from 1985 to 2014 were collected from national meteorological agency. The quantitative and qualitative data were analyzed and interpreted using appropriate analytical tools and procedures.

Findings
The result revealed that the study area is hard hit by moisture stress, due to the late onset of rainy seasons, decrease in the number of rainy days and volume of rainfall. The rainfall distribution behavior coupled with the parallel increase in minimum and maximum temperature exacerbated the impact on livestock system and livestock health. Majority of the pastoralists are found to have rightly perceived the very occurrence and manifestations of climate variability and its consequences. Pastoralists are hardly coping with the challenges of climate variability, mainly due to cultural prejudice, poor service delivery and the socio-economic and demographic challenges.

Research limitations/implications
Pastoralists are vulnerable to the adverse impact of climate variability and extreme events.

Practical implications
The finding of the study provides baseline information for practitioners, researchers and policymakers.

Originality/value
This paper provided detailed insights about the rainfall and temperature trend and variability for the past three decades. The finding pointed that pastoralists’ livelihood is under climate variability stress, and it has implications to food insecurity.