bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant Chimeras: the good, the bad, and the ‘Bizzaria’
Authors: Frank Margaret H. , Chitwood Daniel H. 
Published: June 2016

AbstractChimeras – organisms that are composed of cells of more than one genotype – captured the human imagination long before they were formally described and used in the laboratory. These organisms owe their namesake to a fire-breathing monster from Greek mythology that has the head of a lion, the body of a goat, and the tail of a serpent. The first description of a non-fictional chimera dates back to the middle of the seventeenth century when the Florentine gardener Pietro Nati discovered an adventitious shoot growing from the graft junction between sour orange (Citrus aurantium) and citron (C. medica). This perplexing chimera that grows with sectors phenotypically resembling each of the citrus progenitors inspired discussion and wonder from the scientific community and was fittingly named the ‘Bizzaria’. Initially, the ‘Bizzaria’ was believed to be an asexual hybrid that formed from a cellular fusion between the grafted parents; however, in-depth cellular analyses carried out centuries later demonstrated that the ‘Bizzaria’, along with other chimeras, owe their unique sectored appearance to a conglomeration of cells from the two donors. Since this pivotal discovery at the turn of the twentieth century, chimeras have served both as tools and as unique biological phenomena that have contributed to our understanding of plant development at the cellular, tissue, and organismal level. Rapid advancements in genome sequencing technologies have enabled the establishment of new model species with novel morphological and developmental features that enable the generation of chimeric organisms. In this review, we show that genetic mosaic and chimera studies provide a technologically simple way to delve into the organismal, genetic, and genomic inner workings underlying the development of diverse model organisms. Moreover, we discuss the unique opportunity that chimeras present to explore universal principles governing intercellular communication and the coordination of organismal biology in a heterogenomic landscape.
fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets
Authors: Madrigal Pedro 
Published: June 2016

AbstractSummaryComputational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomic science, as it allows both to evaluate the reproducibility across biological or technical replicates, and to compare different datasets to identify their potential correlations. Here I present fCCAC, an application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). I exemplify how this method can reveal shared covariance between histone modifications and DNA binding proteins, such as the relationship between the H3K4me3 chromatin mark and its epigenetic writers and readers.AvailabilityR code is publicly available athttp://github.com/pmb59/fCCAC/.Contactpm12@sanger.ac.uk
C. eleganschromosomes connect to centrosomes by anchoring into the spindle network
Authors: Redemann Stefanie , Baumgart Johannes , Lindow Norbert , Fürthauer Sebastian , Nazockdast Ehssan , Kratz Andrea , Prohaska Steffen , Brugués Jan , Shelley Michael , Müller-Reichert Thomas 
Published: June 2016

AbstractThe mitotic spindle ensures the faithful segregation of chromosomes. To discover the nature of the crucial centrosome-to-chromosome connection during mitosis, we combined the first large-scale serial electron tomography of whole mitotic spindles in earlyC. elegansembryos with live-cell imaging. Using tomography, we reconstructed the positions of all microtubules in 3D, and identified their plus- and minus-ends. We classified them as kinetochore (KMTs), spindle (SMTs), or astral microtubules (AMTs) according to their positions, and quantified distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs are directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient.
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
Authors: Tørresen Ole K. , Star Bastiaan , Jentoft Sissel , Reinar William B. , Grove Harald , Miller Jason R. , Walenz Brian P. , Knight James , Ekholm Jenny M. , Peluso Paul , Edvardsen Rolf B. , Tooming-Klunderud Ave , Skage Morten , Lien Sigbjørn , Jakobsen Kjetill S. , Nederbragt Alexander J. 
Published: June 2016

AbstractBackground: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.Results: By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21 % of the TRs across the assembly, 19 % in the promoter regions and 12 % in the coding sequences are heterozygous in the sequenced individual.Conclusions: The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.
Tax policy and farm capital investment: Section 179 expensing and bonus depreciation
Authors: Williamson James M , Stutzman Sarah 
Published: June 2016

Purpose– The purpose of this paper is to estimate the impact of Internal Revenue Code cost recovery provisions – Section 179 and “bonus depreciation” – on farm capital investment.Design/methodology/approach– The authors construct a synthetic panel of data consisting of cohorts of similar farms based on state and production specialization using the USDA’s Agricultural Resource Management Survey for years 1996-2012. Employing panel data methods, the authors are able to control for time-invariant fixed effects, as well as the effects of past investment on current investment.Findings– The authors estimate statistically significant investment demand elasticities with respect to the Section 179 expensing deduction of between 0.28 and 0.50. A change in bonus depreciation, on average, had little impact on capital investment.Practical implications– The estimates suggest there is a modest effect of the cost recovery provisions on investment overall, but a stronger effect on farms that have more than $10,000 in gross cash farm income. There are other implications for the agricultural sector: the provisions may encourage technology adoption with its associated benefits, such as reduced cost of production and improved conservation practices. On the other hand, the policy could contribute to the growing concentration in production as large commercial farms expand their operated acreage to take advantage of increasingly efficient physical capital.Originality/value– To the authors’ knowledge, this is the first research to use a nationally representative dataset to estimate to impact of Section 179 and “bonus depreciation” on farm investment. The findings provide evidence of the provisions’ impact on farm capital purchases.
Land titles and formal credit in Thailand
Authors: Sakprachawut Soontaree , Jourdain Damien 
Published: June 2016

Purpose
– The purpose of this paper is to investigate the effects of land titles and farmers’ characteristics on their participation in the formal credit market in a land reform area of Thailand.

Design/methodology/approach
– Data collected on 218 farm households in one land reform area of Western Thailand are analyzed with a generalized double-hurdle model to calculate the probability of farm households to take a loan and the size of the loans from a formal credit institute, the Bank for Agriculture and Agricultural Co-operatives.

Findings
– The results suggest that the absence of a title, whether fully or partially transferable, decreases significantly the participation to the formal credit market and the size of the loans. However, this effect was small. The findings also indicate that the farm assets, household head’s gender and age, and the labor force per hectare were significantly influencing the probability of participation to borrow money as well as the amount borrowed.

Practical implications
– The possibility given to farmers having title with partial transferability to provide alternative types of guarantees reduced the gap in loan-taking between the different types of land title. However, the presence of a land title, transferable or not, had a significant influence on farmers demand and success in obtaining credit.

Originality/value
– The paper investigates the possible effects of a unique partial land rights in Thailand that guarantees only security of use of the land but prohibits sale.
The impact of higher education commission of pakistan’s funding on the collection development budgets of university libraries
Authors: Khan Ghalib , Bhatti Rubina 
Published: June 2016

Purpose
This study aims to investigate the annual financial management of university libraries in the province of Khyber Pakhtunkhwa (KPK), Pakistan, and its relationship with Higher Education Commission (HEC) grants to examine libraries’ share.

Design/methodology/approach
Using survey methods, this study explores the annual budget allocation of well-established university libraries in the province of KPK in the past five years and its relationship with HEC grants to determine libraries’ shares. The survey followed a qualitative design based on an interview technique of data collection. The scope of this study covers all those public sector universities which are chartered by the Government of KPK, recognized by HEC, and eligible for HEC grants on annual basis. Based on this formulation, 15 public sector universities were selected for the survey.

Findings
The data analysis of the present study revealed that no specific norms are followed by the university administrations in allocating funds for libraries out of HEC annual grants. University libraries in the province either do not have funding polices or are administered by the concerned establishments where Library and Information Science professionals have no role in the financial management of libraries. The study also found that university administrations in KPK either do not provide sufficient share to libraries out of HEC grants or specify an inadequate share which is in violation of the clear instructions of HEC ordinance 2002, Section 10(h).

Originality/value
This study is the first of its kind in Pakistan as it provides an insight into how much budget is allocated for collection development in the university libraries, compares it with HEC grants to calculate libraries’ share in percentage and suggests to the HEC to encourage university administration to allocate sufficient budget for libraries to improve collection development, service provision, acquisition, selection and patronage.
Can we shift more library costs to students?
Authors: Steele Kirstin 
Published: June 2016

Purpose
The purpose of the study is to discuss Questia, a library database that is marketed directly to student users.

Design/methodology/approach
Opinion piece.

Findings
From a student’s perspective, Questia is very useful. It would not be a useful addition to undergraduate libraries, even if site licenses are available.

Research limitations/implications
It would be interesting to design a study to compare library skills of undergraduates who are subscribed to Questia with those who participate in traditional library instruction sessions.

Practical implications
It is suggested that Questia should be recommended to an undergraduate student who is struggling with basic research skills or who is especially pressed for time.

Originality/value
There are no scholarly articles discussing Questia after 2012.
Multisource system for NDT of welded elements exploited in aircraft industry
Authors: Chady Tomasz , Sikora Ryszard , Szwagiel Mariusz , Grzywacz Bogdan , Misztal Leszek , Waszczuk Pawel , Szydlowski Michal , Szymanik Barbara 
Published: June 2016

Purpose
– The purpose of this paper is to describe a multisource system for nondestructive inspection of welded elements exploited in aircraft industry developed in West Pomeranian University of Technology, Szczecin in the frame of CASELOT project. The system task is to support the operator in flaws identification of welded aircraft elements using data obtained from X-ray inspection and 3D triangulation laser scanners.

Design/methodology/approach
– For proper defects detection a set of special processing algorithms were developed. For easier system exploitation and integration of all components a user friendly interface in LabVIEW environment was designed.

Findings
– It is possible to create the fully independent, intelligent system for welds’ flaws detection. This kind of technology might be crucial in further development of aircraft industry.

Originality/value
– In this paper a number of innovative solutions (new algorithms, algorithms’ combinations) for defects’ detection in welds are presented. All of these solutions are the basis of presented complete system. One of the main original solution is a combination of the systems based on 3D triangulation laser scanner and X-ray testing.
Finite element analysis of the active element displacement in a giant magnetostrictive transducer
Authors: Stachowiak Dorota 
Published: June 2016

Purpose– The purpose of this paper is to find the method for determining the displacement of the active element in a giant magnetostrictive transducer.Design/methodology/approach– The giant magnetostrictive transducer with the active element made of Terfenol-D has been considered. A structure with an axisymmetrical transducer has been proposed. In the proposed model the coupling of magnetic and mechanical field has been taken into account. Maxwell’s equations for electromagnetics and Navier’s equations for mechanical systems are formulated in weak form and coupled using a nonlinear magneto-mechanical constitutive law for Terfenol-D. In order to obtain the distribution of the magnetic and mechanical fields the finite element method was used. The elaborated nonlinear magnetostrictive model has been implemented by using a finite element weak formulation with COMSOL Multiphysics.Findings– The elaborated model for the giant magnetostrictive transducer allows to take into account the magneto-mechanical coupling as well as the material’s nonlinearity. The calculation results of the strain distributions caused by magnetostrictive forces have been presented. The output displacement of a transducer vs supply current for different compressive preload stresses has been calculated and measured. The simulation and measurements results are in close agreement.Research limitations/implications– Taking advantage of the geometrical structure of the prototype of the giant magnetostrictive transducer the computations are performed in an axial-symmetric domain with cylindrical coordinates (r, z, ϑ). The axisymmetric formulation describes the giant magnetostrictive transducers (GMT) without significant loss of accuracy. This approach leads to smaller numerical models and reduced computational time.Practical implications– The elaborated magneto-mechanical model can be used to the design and optimize the structure of GMT.Originality/value– The paper offers the magneto-mechanical model of the giant magnetostrictive transducer. The elaborated model can predict behavior of the magnetostrictive materials it can be used as a tool for the design process of the giant magnetostrictive transducer.
Closed loop voltage control of a solenoid using parallel finite element method
Authors: Marcsa Daniel , Kuczmann Miklós 
Published: June 2016

Purpose– The purpose of this paper is to present the importance of model accuracy in closed loop control by the help of parallel finite element model of a voltage-fed solenoid with iron core.Design/methodology/approach– The axisymmetric formulation of the domain decomposition-based circuit-coupled finite element method (FEM) is embedded in a closed loop control system. The control parameters for the proportional-integral (PI) controller were estimated using the step response of the analytical, static and dynamic model of the solenoid. The controller measures the error of the output of the model after each time step and controls the applied voltage to reach the steady state as fast as possible.Findings– The results of the closed loop system simulation show why the model accuracy is important in the stage of the controller design. The FEM offers higher accuracy that the analytic model attained with magnetic circuit theory, because the inductance and resistance variation already take into account in the numerical calculation. Furthermore, parallel FEM incorporating domain decomposition to reduce the increased computation time.Originality/value– A closed loop control with PI controllers is applied for a voltage driven finite element model. The high computation time of the numerical model in the control loop is decreased by the finite element tearing and interconnecting method with direct and iterative solver.
Piezoelectrically programmable electric-field driven LC (ELC) resonators acting as THz modulators
Authors: Lalas Antonios X. , Kantartzis Nikolaos V. , Tsiboukis Theodoros D. 
Published: June 2016

Purpose– Metamaterials are artificially tailored complex media with extraordinary properties, not available in nature. Due to their unique performance, they are considered as a crucial component of modern radio-frequency technology, especially in the THz regime. However, their lack of wide spectral bandwidths introduce constraints for realistic applications. The purpose of this paper is to propose piezoelectric micro-electromechanical systems (MEMS) actuators to modify the shape of electric field-driven LC (ELC) resonators. A THz modulation capability is revealed by connecting/disconnecting the associated metal parts.Design/methodology/approach– Piezoelectric MEMS actuators are proposed to provide the desired bandwidth enhancement along with THz modulation. Two setups with different degrees of freedom in altering the behaviour of the novel modulator are investigated. A variety of numerical data, acquired via the finite element method, substantiate the advantageous characteristics of the proposed structures.Findings– The novel devices enable the modification of the structural features of an ELC-based complex medium, unveiling in this manner a significant THz modulation capability along with improved bandwidth tunability. Two discrete cases are presented involving different degrees of freedom to shape the overall performance of the metamaterial modulator.Originality/value– Development of a THz modulator, which utilises metamaterials as its fundamental component. Incorporation of tunable piezoelectric metamaterials into THz technology allowing increased reconfigurability. Bandwidth enhancement of metamaterial systems and alternative design via multiple controllable gaps enabling more degrees of freedom for design purposes.
The depiction of marketing and marketers in the news media
Authors: Cluley Robert 
Published: June 2016

Purpose
In an effort to explain the high level of scepticism and distrust towards marketing and marketers, this paper aims to explore how marketing practice and practitioners are depicted in the mass media.

Design/methodology/approach
The paper analyses 6,877 news reports that discuss “marketing” across two one-year time periods from three UK newspapers. A systematic content analysis is presented through N-grams and K-grams, close readings of individual cases and manual coding.

Findings
The paper finds that the news media cultivates an image of marketing and marketing practitioners as a cost to businesses and something that businesses do to consumers. The study finds that marketers are also presented through a narrow viewpoint. Marketers are depicted as male and tend to be viewed as a source of authority only when speaking on behalf of their organizations in response problems and crises.

Research limitations/implications
The cultivation effect of mass media is widely accepted among communications scholar, yet its use within marketing research is limited. The paper represents an empirical application of this approach.

Practical implications
Organizations including the Chartered Institute of Marketing and American Marketing Association have attempted to counteract marketing’s image problem by redefining what marketing means. The results of this study suggest that such attempts are unlikely to work, as the practice of marketing, in particular PR, cultivates a negative image in the media.

Social implications
The paper explores the relationship between marketing practice and the marketing profession and society.

Originality/value
The paper demonstrates the utility of cultivation theory and systematic content analyses of media texts. It develops a methodology to examine how professional practice is depicted in mass media.
The evolving family assemblage: how senior families “do” family
Authors: Huff Aimee Dinnin , Cotte June 
Published: June 2016

Purpose
A growing stream of consumer research has examined the intersection of family dynamics, consumption practices and the marketplace. The purpose of this paper is to make sense of the complex nature of family for senior families (adult children and their elderly parents) who employ the use of elder care services and facilities.

Design/methodology/approach
This research analyses data gathered from in-depth interviews with adult siblings and their elderly parents through the lens of assemblage theory.

Findings
This paper advances a conceptulisation of the family as an evolving assemblage of components, including individual members; material possessions and home(s); shared values, goals, memories and practices; prominent familial attributes of love and care; and marketplace resources. Three features of the assemblage come to the fore in senior families: the fluid meaning of independence for the elderly parent, the evolution of shared family practices and the trajectory of the assemblage that is a function of its history and future.

Originality/value
This research focuses on a stage of family life that has been under-theorised; applies assemblage theory to the family collective, demonstrating that a family can be conceptualised as an ever-evolving assemblage of human and non-human components, and this is a useful lens for understanding how senior families “do” family; and argues for a broader notion of family – one that is not household-centric or focused on families with young children, that encompasses members and materiality and that foregrounds the dynamic, evolving nature of family life.