bluuebunny/crossref_metadata_2025 huggingface dataset:
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
Authors: Zuin Jessica , Dixon Jesse R. , van der Reijden Michael I. J. A. , Ye Zhen , Kolovos Petros , Brouwer Rutger W. W. , van de Corput Mariëtte P. C. , van de Werken Harmen J. G. , Knoch Tobias A. , van IJcken Wilfred F. J. , Grosveld Frank G. , Ren Bing , Wendt Kerstin S.
Published: December 2013

Significance

For the 2m DNA to fit into the tiny cell nucleus, it is wrapped around nucleosomes and folded into loops clustering together in domains. Genome function depends on this 3D-organization, especially on-going dynamic processes like transcription. Techniques studying the network of DNA contacts genome-wide have recently revealed this 3D architecture, but the protein factors behind this are not understood. We study two proteins that are known to help form DNA loops: cohesin and CTCC-binding factor (CTCF). Respective depletion and analysis of DNA contacts genome-wide show that CTCF is required to separate neighboring folding domains and keep cohesin in place, whereas cohesin is important for shaping the domains. Consistently, we observe different changes of gene expression.
‘Positioning’ in the conversation analytic approach
Authors: Day Dennis , Kjaerbeck Susanne
Published: December 2013

From the perspective of ethnomethodology and conversation analysis (EM/CA), the concept of positioning may offer a compellingly rich metaphor for understanding identity and relations. There appears, however, to be no such analytical concept in EM/CA. Instead, the EM/CA approach offers concepts such as alignment-affiliation, identities and membership categories — all of them based on actional resources on the micro-level of talk. The aim of this article is to inquire if EM/CA tools for the analysis of identities and relations in talk might be considered interesting from the perspective of positioning theory. To do so, we offer EM/CA analyses of narrative and non-narrative data in which the in situ negotiation of identities and relations plays a major role.
Building iterativity into positioning analysis
Authors: Georgakopoulou Alexandra
Published: December 2013

The aim of this chapter is to contribute to the ongoing debate within interactional approaches to positioning in narrative regarding the ways in which we can analytically tap into aspects of teller’s self that can be seen as stable or continuous. Bamberg’s level 3 positioning which answers the question of ‘Who am I?” has inspired a lot of those discussion and it forms a productive point of departure here too. I attempt to systematize the exploration of Level 3 with a practice-based approach to narrative that: (a) affords ethnographically grounded understandings of who people are in specific contexts, (b) places narrative analysis within a multi-method that ensures access to the participants’ moments of reflexivity on themselves and their stories. I pose ways of telling, sites and tellers as the main constituent elements of such an approach and argue that iterativity is the key-element in the exploration of all three and ultimately in the uncovery of aspects of self that are presented as relatively stable. I base my discussion on data from a study of pupils in a London senior (sic high) school and single out breaking news about the participants’ new media engagements as a significant narrative activity for positioning.
Positioning identities
Authors: Korobov Neill
Published: December 2013

The purpose of this article is to broaden and sharpen the use of positioning in social science inquiry. Historically, positioning has either been aligned with ethogenic and ontological constructionist views of discourse/identity or post-structural projects interested in positioning as means to uncovering how people’s minds work or how an ordered extant exterior world shapes and constitutes human action. Rather than looking through acts of positioning to minds or worlds, the present chapter offers an epistemic discursive psychological view of positioning as sets of local discursive processes whereby speakers elegantly exploit the features of ordinary talk so as to make relevant their own and/or other’s identities as part of some social business that has an interactional logic as well as here-and-now relational consequences. The discursive dexterity of positioning is illustrated through an analysis of the negotiation of gendered identity categories.
Positioning as membership management
Authors: Quasthoff Uta M.
Published: December 2013

The contribution looks into the mechanisms of interactively establishing identities by managing memberships in the special case of telling a researcher about experiences and assessments with respect to public authorities. Drawing on the particular potential of these data, it is shown how the tasks of assigning memberships and ascribing appropriate category-bound activities are performed within evaluative practices and how general assessments and singular personal experiences are intertwined to position the teller in the ongoing interaction.
Translating a national grand narrative into a personal biographies
Authors: Shoshana Avihu
Published: December 2013

This article examines the connection between grand narratives and the creative ways that individuals translate them into personal biographies through a case study of a boarding school for gifted disadvantaged youth in Israel. To test the state’s grand narrative, I performed a content analysis of minutes of governmental protocols as well as organizational reports at the time the boarding school was established. The state grand narrative stresses the rescue of Jews from Arab countries by the leaders of the state and the linear Oriental-to-Occidental cultural development that these Jews must undergo in order to survive in modern life. To examine the question of how the grand narrative is translated into personal biographies, sixty graduates of the boarding school and thirty-two siblings who did not attend the boarding school were interviewed. The findings demonstrate that the graduates of the boarding school translated the grand narrative into a special narrative configuration known as the alternative biography, a concept that addresses the lifeworlds that, in the subjects’ judgment, might have characterized their lives under different circumstances. Further, the structure of this narrative points to one explicit alternative biography, that of the sibling who did not attend the boarding school. The disscusion chapter explores the phenomenological meanings of this singular narrative configuration.
From small stories to networked narrative
Authors: Page Ruth , Harper Richard , Frobenius Maximiliane
Published: December 2013

This article addresses the emergence of networked narration found in Facebook updates. Drawing on anthropological approaches to co-tellership (Ochs & Capps, 2001), we trace how storyworlds are co-constructed by multiple narrators via the communicative affordances which have developed in the Facebook status update: namely, the practices of commenting, liking, linking, tagging, photo-sharing, and marking geographical location. Our longitudinal analysis of 1800 updates elicited from 60 participants over a period of four years suggests that the rise of what we call a ‘networked narrative’ allows individuals to participate collectively in the construction of ‘shared stories’ (Georgakopoulou, 2007), and through this process for narrators to co-construct their social identities through their interactions with others. We argue that the distribution of storytelling as it takes place on Facebook may be found in other online and offline contexts, and challenges earlier, linear models of narrative form that have dominated discourse-analytic and literary-critical narratology.
The attraction of tragic narrative
Authors: Koopman Emy
Published: December 2013

A survey study was conducted to explore why people read about suffering, giving particular attention to the role that catharsis may play. Through an online questionnaire, respondents (N = 67) commented on a popular autobiographical Dutch novel about grief. The questionnaire contained closed and open questions, addressing motives for reading and thoughts and feelings while reading. Results indicated that curiosity about content, style and the author, fueled by media-attention and the author’s status, were the most important motives for reading the novel. Respondents who had experienced a significant loss themselves demonstrated a need for recognition and support. Responses further suggested that “clarification” (gaining deep insight) is a better explanation for the attraction of tragic narrative than “purgation.” Clarification did not appear to be related to fear, and the role of empathic emotions appeared questionable. Cluster analysis did identify a potential “catharsis group,” which combined fear, pity and appreciation for the articulation of grief.
Effects of loss and trauma on sublime disquietude during literary reading
Authors: Kuiken Don , Sharma Ruby
Published: December 2013

Two studies of literary reading described the effects of loss, trauma, and traumatic loss on moments of disclosure during expressive engagement with the text. Study 1 compared readers who had experienced recent loss, recent trauma or neither recent loss nor trauma. Study 2 extended this paradigm to include traumatic loss. Dependent variables included an index of sublime disquietude, specifically, the interactive combination of perceived discord, self-perceptual depth, and inexpressible realizations. Across both studies, (1) a combination of traumatic distress and separation distress predicted sublime disquietude; (2) dissociation (depersonalization, amnesia) predicted sublime disquietude; and (3) distress in response to loss, trauma, or traumatic loss motivated reading at the limits of expressibility. This pattern of results is described in relation to Heidegger’s (1962) characterization of how, within being-toward-death, an uncanny not-at-homeness (Unheimlichkeit) is the context within which an experiential process provides an unsettling and yet elevating disclosure of finitude.
Predation and protists
Authors: Kirchman David L.
Published: December 2013

This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis-Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about 10-fold smaller than the equivalent spherical diameter of the protistan predator. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world, and are critical links between microbial food chains and larger organisms. Many protists, especially in aquatic habitats, are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested, photosynthetic prey or its chloroplasts.
Darting, anesthesia, and handling
Authors: Glander Kenneth E.
Published: December 2013

Capture of non-human primates is the only way that research questions requiring unequivocal identification can be answered. Much of the current research on primates remains cross-sectional and of short duration. In addition, capture is the only way to take advantage of the ongoing revolution in miniaturization that allows the use of lab-based technologies on wild primates. These physiological data provide insight on how behaviour is related to variable weather conditions, available energy, and food choices, thus, relating environmental variation to behavioural and physiological data. The behaviour and physiology of free-ranging primates results from the interaction of numerous factors that cannot be adequately replicated in the laboratory. These factors include food supply, food quality, predation, social interactions, and three-dimensional variation in forest weather conditions. Thus, existing data from lab studies may not provide an ecologically, and therefore evolutionarily, relevant explanation of most primate behaviour or physiology in response to environmental variation. This chapter outlines methods for the capture of non-human primates including darting, anaesthesia, and handling, including general recommendations for drug dosages as well as approaches to ensure the safety of the handler(s).
Econophysics and Physical Economics
Authors: Richmond Peter , Mimkes Jürgen , Hutzler Stefan
Published: December 2013

An understanding of the behaviour of financial assets and the evolution of economies has never been as important as it is today. This book looks at these complex systems from the perspective of the physicist. So-called ‘econophysics’ and its application to finance have made great strides in recent years. Less emphasis has been placed on the broader subject of macroeconomics, and many economics students are still taught traditional neo-classical economics. The reader is given a general primer in statistical physics, probability theory, and use of correlation functions. Much of the mathematics that is developed is frequently no longer included in undergraduate physics courses. The statistical physics of Boltzmann and Gibbs is one of the oldest disciplines within physics and it can be argued that it was first applied to ensembles of molecules as opposed to being applied to social agents only by way of historical accident. The authors argue by analogy that the theory can be applied directly to economic systems comprising assemblies of interacting agents. The necessary tools and mathematics are developed in a clear and concise manner. The body of work, now termed econophysics, is then developed. The authors show where traditional methods break down and how the probability distributions and correlation functions can be properly understood using high-frequency data. Recent work by the physics community on risk and market crashes are discussed together with new work on betting markets, as well as studies of speculative peaks that occur in housing markets.
PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants
Authors: Li Biao , Wang Gao , Leal Suzanne M.
Published: December 2013

Motivation: Next-generation sequencing and other high-throughput technology advances have promoted great interest in detecting associations between complex traits and genetic variants. Phenotype selection, quality control (QC) and control of confounders are crucial and can have a great impact on the ability to detect associations. Although there are programs to perform association analyses, e.g. PLINK and GenABEL, they cannot be used for comprehensive management and QC of phenotype data. To address this need PhenoMan was developed: to select individuals based on multiple phenotype criteria or population membership; control for missing covariate data; remove related individuals, duplicate samples and individuals with incorrect sex specification; recode primary traits and covariates; transform data; remove or winsorize outliers; select covariates for analysis; and create residuals. To ensure consistency and harmonization between analyses, a report is generated for every dataset. Summary statistics are also provided in graphical or text format. PhenoMan can be used for selection and manipulation of quantitative, disease and control data.

Summary: Phenoman is freeware that provides approaches for efficient exploration and management of phenotype data. Proper QC of phenotypes before proceeding to the association analysis is critical to ensure control of type I and II errors, reliable effect estimates and consistent results between studies. PhenoMan is highly beneficial for the preparation of qualitative and quantitative trait data for association studies using new datasets as well as those obtained from public repositories.

Availability and implementation: code.google.com/p/phenoman

Contact: sleal@bcm.edu
On the universality of I–Love–Q relations in magnetized neutron stars
Authors: Haskell B. , Ciolfi R. , Pannarale F. , Rezzolla L.
Published: December 2013

Recently, general relations among the quadrupole moment (Q), the moment of inertia (I) and the tidal deformability (Love number) of a neutron star were shown to exist. They are nearly independent of the nuclear matter equation of state and would be of great aid in extracting parameters from observed gravitational waves and in testing general relativity. These relations, however, do not account for strong magnetic fields. We consider this problem by studying the effect of a strong magnetic field on slowly rotating relativistic neutron stars and show that, for simple magnetic field configurations that are purely poloidal or purely toroidal, the relation between Q and I is again nearly universal. However, different magnetic field geometries lead to different I–Q relations, and, in the case of a more realistic twisted-torus magnetic field configuration, the relation depends significantly on the equation of state, losing its universality. I–Love–Q relations must thus be used with very great care, since universality is lost for stars with long spin periods, i.e. P ≳ 10 s, and strong magnetic fields, i.e. B ≳ 1012 G.
Analysis of the SWI/SNF chromatin-remodeling complex during early heart development and BAF250a repression cardiac gene transcription during P19 cell differentiation
Authors: Singh Ajeet Pratap , Archer Trevor K.
Published: December 2013

The regulatory networks of differentiation programs and the molecular mechanisms of lineage-specific gene regulation in mammalian embryos remain only partially defined. We document differential expression and temporal switching of BRG1-associated factor (BAF) subunits, core pluripotency factors and cardiac-specific genes during post-implantation development and subsequent early organogenesis. Using affinity purification of BRG1 ATPase coupled to mass spectrometry, we characterized the cardiac-enriched remodeling complexes present in E8.5 mouse embryos. The relative abundance and combinatorial assembly of the BAF subunits provides functional specificity to Switch/Sucrose NonFermentable (SWI/SNF) complexes resulting in a unique gene expression profile in the developing heart. Remarkably, the specific depletion of the BAF250a subunit demonstrated differential effects on cardiac-specific gene expression and resulted in arrhythmic contracting cardiomyocytes in vitro. Indeed, the BAF250a physically interacts and functionally cooperates with Nucleosome Remodeling and Histone Deacetylase (NURD) complex subunits to repressively regulate chromatin structure of the cardiac genes by switching open and poised chromatin marks associated with active and repressed gene expression. Finally, BAF250a expression modulates BRG1 occupancy at the loci of cardiac genes regulatory regions in P19 cell differentiation. These findings reveal specialized and novel cardiac-enriched SWI/SNF chromatin-remodeling complexes, which are required for heart formation and critical for cardiac gene expression regulation at the early stages of heart development.
First Report of Onion yellow dwarf virus, Garlic common latent virus and Shallot latent virus on Garlic in Poland
Authors: Chodorska M. , Paduch-Cichal E. , Kalinowska E. , Szyndel M. S.
Published: December 2013

Garlic (Allium sativum L.) is vegetatively propagated and can be affected by a virus complex (1) consisting of two potyviruses, Onion yellow dwarf virus (OYDV) and Leek yellow stripe virus (LYSV), and two carlaviruses, Garlic common latent virus (GCLV) and Shallot latent virus (SLV) (2). OYDV, GCLV, and SLV are economically important viral pathogens of bulb garlic crops in many garlic-growing areas of the world. A general mosaic and yellowing of leaves of four garlic cultivars (Blanko, Harnaś, Jarus, and Mega) was observed in 11 garlic-production fields in the Lodz, Mazowieckie, Małopolska, and Pomorskie regions of Poland in July 2012. ELISA was carried out with extracts from 29 collected garlic leaf samples to detect OYDV, GCLV, and SLV using commercial antiserum (DSMZ, Braunschweig, Germany). Results indicated that 6 samples (20.7%) were infected with OYDV, 25 samples (86.2%) were infected with GCLV, and 23 samples (79.3%) were infected with SLV. The presence of these viruses in garlic leaf samples was confirmed by reverse transcription (RT)-PCR using total RNA extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich, Munich, Germany) and primers, designed in this study, specific to the whole coat protein gene of OYDV (OYDVF 5′-TAGGGTTGGATTATGATTTCTCGA-3′ and OYDVR 5′-TAGTGGTACACCACATTTCGT-3′), GCLV (GCLVF 5′-TTATAGGGACGGCACAAAATCAATCA-3′ and GCLVR 5′-AATAGCACTCCTAGAACAACCATT-3′) and SLV (SLVF 5′-AATYATTTACAATCGTCCAGCTA-3′ and SLVR 5′-ATAATATCAATCAAATMCACACAATT-3′). Amplicons of the expected size were obtained for each virus. The amplified products were purified and sequenced in both directions. Sequence information of the CP genes of 9 OYDV, 12 GCLV, and 7 SLV isolates has been submitted to NCBI-GenBank with accession numbers KF862683 to KF862710. Sequence analysis showed that the coat protein gene of OYDV shared 86% identity with the coat protein gene of OYDV isolate MS/SW1 from Australia (GenBank Accession No. HQ258894). Comparison of the coat protein gene sequences of Polish GCLV isolates with those available in GenBank showed 85 to 91% sequence identities. Multiple sequence alignment revealed 84% nucleotide identity between the Polish isolate of SLV and an SLV isolate from Chinese garlic (AF314147) formerly referred to as Garlic latent virus (3). To the best of our knowledge, this is the first report of OYDV, GCLV, and SLV in garlic plants in Poland. The accurate identification of viruses present in garlic plants will help to use the appropriate strategies to reduce viral incidence in garlic-growing areas.

References: (1) J. Chen et al. Arch Virol 146:1841, 2001. (2) A. M. G. King et al. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, San Diego, CA, 2011. (3) T. Tsuneyoshi et al. Arch. Virol. 143:1093, 1998.
Automated Near–Real-time Clinical Performance Feedback for Anesthesiology Residents
Authors: Ehrenfeld Jesse M. , McEvoy Matthew D. , Furman William R. , Snyder Dylan , Sandberg Warren S.
Published: December 2013

Background:

Anesthesiology residencies are developing trainee assessment tools to evaluate 25 milestones that map to the six core competencies. The effort will be facilitated by development of automated methods to capture, assess, and report trainee performance to program directors, the Accreditation Council for Graduate Medical Education and the trainees themselves.

Methods:

The authors leveraged a perioperative information management system to develop an automated, near–real-time performance capture and feedback tool that provides objective data on clinical performance and requires minimal administrative effort. Before development, the authors surveyed trainees about satisfaction with clinical performance feedback and about preferences for future feedback.

Results:

Resident performance on 24,154 completed cases has been incorporated into the authors’ automated dashboard, and trainees now have access to their own performance data. Eighty percent (48 of 60) of the residents responded to the feedback survey. Overall, residents “agreed/strongly agreed” that they desire frequent updates on their clinical performance on defined quality metrics and that they desired to see how they compared with the residency as a whole. Before deployment of the new tool, they “disagreed” that they were receiving feedback in a timely manner. Survey results were used to guide the format of the feedback tool that has been implemented.

Conclusion:

The authors demonstrate the implementation of a system that provides near–real-time feedback concerning resident performance on an extensible series of quality metrics, and which is responsive to requests arising from resident feedback about desired reporting mechanisms.
Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy
Authors: Miki Takeshi , Yokokawa Taichi , Matsui Kazuaki
Published: December 2013

Ecosystems have a limited buffering capacity of multiple ecosystem functions against biodiversity loss (i.e. low multifunctional redundancy). We developed a novel theoretical approach to evaluate multifunctional redundancy in a microbial community using the microbial genome database (MBGD) for comparative analysis. In order to fully implement functional information, we defined orthologue richness in a community, each of which is a functionally conservative evolutionary unit in genomes, as an index of community multifunctionality (MF). We constructed a graph of expected orthologue richness in a community (MF) as a function of species richness (SR), fit the power function to SR (i.e. MF =
c
SR

a

), and interpreted the higher exponent
a
as the lower multifunctional redundancy. Through a microcosm experiment, we confirmed that MF defined by orthologue richness could predict the actual multiple functions. We simulated random and non-random community assemblages using full genomic data of 478 prokaryotic species in the MBGD, and determined that the exponent in microbial communities ranged from 0.55 to 0.75. This exponent range provided a quantitative estimate that a 6.6–8.9% loss limit in SR occurred in a microbial community for an MF reduction no greater than 5%, suggesting a non-negligible initial loss effect of microbial diversity on MF.
An Adaptive Threshold in Mammalian Neocortical Evolution
Authors: Lewitus Eric , Kelava Iva , Kalinka Alex T. , Tomancak Pavel , Huttner Wieland B
Published: December 2013

Expansion of the neocortex is a hallmark of human evolution. However, it remains an open question what adaptive mechanisms facilitated its expansion. Here we show, using gyrencephaly index (GI) and other physiological and life-history data for 102 mammalian species, that gyrencephaly is an ancestral mammalian trait. We provide evidence that the evolution of a highly folded neocortex, as observed in humans, requires the traversal of a threshold of ∼109neurons, and that species above and below the threshold exhibit a bimodal distribution of physiological and life-history traits, establishing two phenotypic groups. We identify, using discrete mathematical models, proliferative divisions of pro-genitors in the basal compartment of the developing neocortex as evolutionarily necessary and sufficient for generating a fourteen-fold increase in daily prenatal neuron production and thus traversal of the neuronal threshold. Finally, using RNA-seq data from fetal human neocortical germinal zones, we show a genomic correlate to the neuron threshold in the differential conservation of long intergenic non-coding RNA. (see arXiv:1304.5412)
Hallmarks of a new era in mitochondrial biochemistry
Authors: Pagliarini David J. , Rutter Jared
Published: December 2013

Stemming from the pioneering studies of bioenergetics in the 1950s, 1960s, and 1970s, mitochondria have become ingrained in the collective psyche of scientists as the “powerhouses” of the cell. While this remains a worthy moniker, more recent efforts have revealed that these organelles are home to a vast array of metabolic and signaling processes and possess a proteomic landscape that is both highly varied and largely uncharted. As mitochondrial dysfunction is increasingly being implicated in a spectrum of human diseases, it is imperative that we construct a more complete framework of these organelles by systematically defining the functions of their component parts. Powerful new approaches in biochemistry and systems biology are helping to fill in the gaps.
eIF2B promotes eIF5 dissociation from eIF2•GDP to facilitate guanine nucleotide exchange for translation initiation
Authors: Jennings Martin D. , Zhou Yu , Mohammad-Qureshi Sarah S. , Bennett David , Pavitt Graham D.
Published: December 2013

Protein synthesis factor eIF2 delivers initiator tRNA to the ribosome. Two proteins regulate its G-protein cycle: eIF5 has both GTPase-accelerating protein (GAP) and GDP dissociation inhibitor (GDI) functions, and eIF2B is the guanine nucleotide exchange factor (GEF). In this study, we used protein–protein interaction and nucleotide exchange assays to monitor the kinetics of eIF2 release from the eIF2•GDP/eIF5 GDI complex and determine the effect of eIF2B on this release. We demonstrate that eIF2B has a second activity as a GDI displacement factor (GDF) that can recruit eIF2 from the eIF2•GDP/eIF5 GDI complex prior to GEF action. We found that GDF function is dependent on the eIF2Bɛ and eIF2Bγ subunits and identified a novel eIF2–eIF2Bγ interaction. Furthermore, GDF and GEF activities are shown to be independent. First, eIF2B GDF is insensitive to eIF2α phosphorylation, unlike GEF. Second, we found that eIF2Bγ mutations known to disrupt GCN4 translational control significantly impair GDF activity but not GEF function. Our data therefore define an additional step in the protein synthesis initiation pathway that is important for its proper control. We propose a new model to place eIF2B GDF function in the context of efficient eIF2 recycling and its regulation by eIF2 phosphorylation.
A Conserved KIN17 Curved DNA-Binding Domain Protein Assembles with SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 to Adapt Arabidopsis Growth and Development to Limiting Copper Availability
Authors: Garcia-Molina Antoni , Xing Shuping , Huijser Peter
Published: December 2013

Proper copper (Cu) homeostasis is required by living organisms to maintain essential cellular functions. In the model plant Arabidopsis (Arabidopsis thaliana), the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 (SPL7) transcription factor participates in reprogramming global gene expression during Cu insufficiency in order to improve the metal uptake and prioritize its distribution to Cu proteins of major importance. As a consequence, spl7 null mutants show morphological and physiological disorders during Cu-limited growth, resulting in lower fresh weight, reduced root elongation, and chlorosis. On the other hand, the Arabidopsis KIN17 homolog belongs to a well-conserved family of essential eukaryotic nuclear proteins known to be stress activated and involved in DNA and possibly RNA metabolism in mammals. In the study presented here, we uncovered that Arabidopsis KIN17 participates in promoting the Cu deficiency response by means of a direct interaction with SPL7. Moreover, the double mutant kin17-1 spl7-2 displays an enhanced Cu-dependent phenotype involving growth arrest, oxidative stress, floral bud abortion, and pollen inviability. Taken together, the data presented here provide evidence for SPL7 and KIN17 protein interaction as a point of convergence in response to both Cu deficiency and oxidative stress.
Amyloplast-Localized SUBSTANDARD STARCH GRAIN4 Protein Influences the Size of Starch Grains in Rice Endosperm
Authors: Matsushima Ryo , Maekawa Masahiko , Kusano Miyako , Kondo Hideki , Fujita Naoko , Kawagoe Yasushi , Sakamoto Wataru
Published: December 2013

Starch is a biologically and commercially important polymer of glucose and is synthesized to form starch grains (SGs) inside amyloplasts. Cereal endosperm accumulates starch to levels that are more than 90% of the total weight, and most of the intracellular space is occupied by SGs. The size of SGs differs depending on the plant species and is one of the most important factors for industrial applications of starch. However, the molecular machinery that regulates the size of SGs is unknown. In this study, we report a novel rice (Oryza sativa) mutant called substandard starch grain4 (ssg4) that develops enlarged SGs in the endosperm. Enlargement of SGs in ssg4 was also observed in other starch-accumulating tissues such as pollen grains, root caps, and young pericarps. The SSG4 gene was identified by map-based cloning. SSG4 encodes a protein that contains 2,135 amino acid residues and an amino-terminal amyloplast-targeted sequence. SSG4 contains a domain of unknown function490 that is conserved from bacteria to higher plants. Domain of unknown function490-containing proteins with lengths greater than 2,000 amino acid residues are predominant in photosynthetic organisms such as cyanobacteria and higher plants but are minor in proteobacteria. The results of this study suggest that SSG4 is a novel protein that influences the size of SGs. SSG4 will be a useful molecular tool for future starch breeding and biotechnology.
Perception of political corruption as a function of legislation
Authors: Krambia-Kapardis Maria
Published: December 2013

Purpose

– The main aim of the paper is to determine whether countries with enacted legislation on electoral accountability issues (such as conflict of interest, revolving doors, asset disclosure, lobbying, immunity, political party funding and a code of conduct for politicians) have lower corruption perception than countries that do not have legislation on those variables.

Design/methodology/approach

– The author utilised the corruption reports developed by the corruption country experts appointed by the EU DG Home and carried a correlation analysis between the above variables and the Corruption Perception Index (CPI) developed by Transparency International.

Findings

– A correlation was only found for the asset disclosure variable and CPI. Alternative factors borne out of the literature are briefly discussed and suggestions for future research are made.

Research limitations/implications

– Due to the small sample size (n=26), the statistical analysis that could be carried out was limited.

Practical implications

– One policy implication of the negative finding obtained is that politicians are well advised to invest in measures that will enhance the electorate's trust in them. Passing anti-corruption legislation alone does not yield low corruption perception.

Originality/value

– This is the first study of its kind addressing corruption correlates by looking at electorate accountability.
Improving internal consistency in IC research and practice: IC and the theory of the firm
Authors: Marzo Giuseppe
Published: December 2013

Purpose

– The purpose of this paper is to demonstrate the usefulness of referring to a theory of the firm as a way to strongly improve internal consistency in both research and practice. To this end, the paper explores how a theory-of-the-firm perspective can assist in a consistent analysis of IC, focusing on five IC-related issues: the definition and the origins of IC; the set of property rights on IC; its role in the competitive advantage and the value generation process of the firm; the way IC can be valued, including issues relating to the internal and external reporting; and finally the most efficient way to effectively manage and control IC. Analysis is carried out referring to the strengths and weaknesses of the resource-based view (RBV), being the main reference theories for IC scholars and practitioners.

Design/methodology/approach

– The paper employs a deductive approach to explore how different theories of the firm shape the way IC-related issues could be consistently analysed.

Findings

– The research finds that referring to a theory of the firm assists investigating IC-related issues. It carries out the analysis of five important issues under the two forms of the RBV, demonstrating how a different theory of the firm differentiates analysis and offers room for improving the internal consistency for both research and practice.

Research limitations/implications

– Implications of the paper are mainly for improving consistency in research, but they also support practice as for consciousness and awareness. Limitations are as follows. First, the paper offers an analysis of only two selected theories of the firm. Second, the analysis is based on a deductive reasoning which can be criticised for the results, even if not for the aim.

Practical implications

– The paper offer stimuli to both theoretical and empirical research and practice. As for research, the paper highlights how consistency can be developed and also focusses on the way empirical research could be consistently carried out. As for practitioners, the paper assists in enlightening covered links between practice and theories.

Originality/value

– The paper pays attention to the role of the theory of the firm, as a way for improving internal consistency in the study and the practice of IC.
Intellectual capital vs the book-value of assets
Authors: Ho Kim Sang , Taylor Dennis
Published: December 2013

Purpose

– The purpose of this paper is to provide new evidence, made possible by human capital data that became available after IFRS adoption, on the productivity of intellectual capital and its components. These productivity measures are modelled to determine their value-relevance in the share market, and the modelling is extended to comparative productivity measures for the book-value of assets.

Design/methodology/approach

– Financial data are sourced from financial databases and company annual reports on a sample of 160 Australian listed firms over a five-year period. Panel regression analysis is used to test five models built from Riahi-Belkaoui's (1999) general price model of the value-relevance of accounting numbers.

Findings

– The results show that the productivity of human capital, structural capital and intellectual capital are each significantly positively related to share price (i.e. have value-relevance), whereas the productivity of total assets at book-value is non-significant and tangible assets is inversely significant.

Originality/value

– This study constructs a new improved method of computing the amount of structural capital, and uses recently available financial statement data to provide first-time evidence on human capital and its inclusion in the determination of the amount of intellectual capital. These new models and data enable a direct comparison to be made between the value-relevance of intellectual and the book-value of assets.
Improving the information environment for analysts
Authors: Farooq Omar , Nielsen Christian
Published: December 2013

Purpose

– The purpose of this paper is to document the relationship between intellectual capital disclosure and analyst following for biotechnology firms listed on the Copenhagen Stock Exchange between 2001 and 2010.

Design/methodology/approach

– Intellectual capital disclosure was computed from financial statements applying the disclosure index of Bukhet al.(2005), while analyst following data were retrieved from the Institutional Brokers’ Estimate System (I/B/E/S).

Findings

– The results show that analysts are more likely to follow firms with high intellectual capital disclosure. This finding suggests that analysts wish to follow those firms for which they have more information. The results also show that the most important intellectual capital disclosures for analysts are those related to employees and strategic statements. This paper therefore expands on previous results by raising awareness of which information companies should disclose to the capital market in order to improve analyst following, in turn helping to improve the general disclosure environment.

Research limitations/implications

– More relevant methods, such as surveys or interviews with management, could be used to improve the information content of intellectual capital disclosure. Analysts probably deduce the intellectual capital of a firm from interaction with management rather than financial statements.

Practical implications

– Firms in and beyond the biotechnology sector can improve their information environment by disclosing more information on intellectual capital in relation to employees and strategic statements in their financial statements.

Originality/value

– The findings shed light on the importance of understanding intellectual capital in the biotechnology sector for analysts and investors who wish to value such firms.
Geographic differences and microevolutionary changes in thermal sensitivity of butterfly larvae in response to climate
Authors: Higgins Jessica K. , MacLean Heidi J. , Buckley Lauren B. , Kingsolver Joel G.
Published: December 2013

Rapid evolution of physiological traits in response to novel thermal environments has rarely been demonstrated in natural populations.

We studied the temperature dependence [thermal performance curves (TPCs)] of larval feeding rate for two populations each of Colias eurytheme and Colias eriphyle in North America that occur over a range of elevations and climates. Using historical data for two of the populations, we assessed changes over time in both air temperatures and TPCs for larval feeding.

Populations at lower elevations with longer growing seasons had broader TPCs for larval feeding. In contrast, higher elevation populations with shorter growing seasons had higher optimal and maximal temperatures for feeding.

Overall mean air temperatures during the growing season showed little change at the two sites, but the frequency of high air temperatures (>28 °C) has increased markedly at both sites over the past 40 years. This climatic shift was associated with increased rates of larval feeding at higher temperatures (>28 °C) in both populations.

These results suggest that recent climate warming has led to physiological shifts in the TPCs for larval feeding in this system, indicating that thermal adaptation can occur rapidly in response to changing thermal conditions.
Offshore marine renewable energy devices as stepping stones across biogeographical boundaries
Authors: Adams Thomas P. , Miller Raeanne G. , Aleynik Dmitry , Burrows Michael T.
Published: December 2013

Offshore renewable energy provides an increasing component of our electricity supply. We have limited understanding of the potential environmental impacts of these developments, particularly in the move to larger scales. Surfaces provided by devices offer novel habitat to marine organisms, which may allow species to spread to new areas.

We used coupled biological and hydrodynamic models to investigate the spread of intertidal marine organisms with pelagic larvae (such as barnacles or gastropods) in the region around south‐western Scotland. We assessed the impact of novel habitat on dispersal and its role in allowing transgression of physical barriers.

Model renewable energy device sites provided habitat for pelagic larval particles that would otherwise have been lost offshore. They also provided a source of larvae for existing coastal sites.

Many offshore devices fulfilled source and destination (or intermediate connection) roles, creating new dispersal pathways, and allowing previously impossible northward dispersal from the Northern Irish coast to Scotland.

Synthesis and applications. New habitat close to biogeographical barriers has implications for existing species’ distributions and genetic population structure. It also affects the spread of non‐native species and ‘climate migrants’. Monitoring these sites for the presence of such species will be important in determining the future ecology of coastal habitat and in maintaining economic aquaculture and marina operations. Future model studies should focus on particular species of importance, taking account of their biology and current distribution.
Managerial Delegation, Cost Asymmetry and Social Efficiency of Entry
Authors: Mukherjee Arijit , Tsai Yingyi
Published: December 2013

This article examines the welfare implications of entry in oligopolistic markets with separation of management from ownership. In the presence of strategic managerial delegation and cost asymmetry, entry is socially insufficient unless the degree of scale economies is large. This result is in stark contrast to those documented in the extant literature. A key feature of our analysis is that a ‘business stealing’ effect (Mankiw & Whinston, 1986) does not arise for the relatively cost‐efficient entrant under managerial delegation. The policy implication emerging from our analysis suggests that entry should be encouraged in industries with strategic managerial delegation, cost asymmetry and not large‐scale economies.
Squeezed in and squeezed out: the effects of population ageing on the demand for housing
Authors: Coleman Andrew
Published: December 2013

This article examines how increasing longevity affects the housing choices of working age and retired people using a heterogeneous agent overlapping generations model that incorporates owner‐occupier and rental sectors, credit constraints, detailed tax regulations and a housing supply sector. Increasing longevity generally leads to declining home ownership rates among young people, with bigger declines if the government increases taxes and pensions rather than relying on additional private provision of retirement income. The model suggests raising tax rates to provide pensions can reduce the welfare of all agents, even those who are net beneficiaries, because they tighten credit constraints on young people.
Economic Inequality in Australia between 1983 and 2010: A Stochastic Dominance Analysis
Authors: Valenzuela Ma. Rebecca , Lean Hooi Hooi , Athanasopoulos George
Published: December 2013

We employ stochastic dominance (SD) analysis on Australian unit records to investigate trends in inequality and relative welfare levels in Australia from 1983 to 2010. Using both income and expenditure distributions, we found that the economy was on a steady descent towards greater inequality between 1983 and 1993, and that this was followed by a 10‐year period of recovery and growth, and gradual improvements in inequality levels. The economy's path to sustainable and equitable growth carried on towards the late 2000s, but this was interrupted by the 2007–08 global financial crisis which caused income inequality levels to deteriorate. Our SD tests show that the country's tax and transfer programmes have been consistent in moderating elevated levels of inequities observed in incomes over time, particularly in periods following economic contraction. Our subgroup results also show strong evidence of long‐term disparities in the relative welfare levels of male‐headed over female‐headed households, of households with children over those without, and of couple‐parents families over their single‐parent counterparts.
Factors Associated with Prolonged Observation Services Stays and the Impact of Long Stays on Patient Cost
Authors: Hockenberry Jason M. , Mutter Ryan , Barrett Marguerite , Parlato Judy , Ross Michael A.
Published: December 2013

Background

Patients are treated using observation services (OS) when their care needs exceed standard outpatient care (i.e., clinic or emergency department) but do not qualify for admission. Medicare and other private payers seek to limit this care setting to 48 hours.

Data Source/Study Setting

Healthcare Cost and Utilization Project data from 10 states and data collected from two additional states for 2009.

Study Design

Bivariate analyses and hierarchical linear modeling were used to examine patient‐ and hospital‐level predictors of OS stays exceeding 48 (and 72) hours (prolonged OS). Hierarchical models were used to examine the additional cost associated with longer OS stays.

Principal Findings

Of the 696,732 patient OS stays, 8.8 percent were for visits exceeding 48 hours. Having Medicaid or no insurance, a condition associated with no OS treatment protocol, and being discharged to skilled nursing were associated with having a prolonged OS stay. Among Medicare patients, the mean charge for OS stays was $10,373. OS visits of 48–72 hours were associated with a 42 percent increase in costs; visits exceeding 72 hours were associated with a 61 percent increase in costs.

Conclusion

Patient cost sharing for most OS stays of less than 24 hours is lower than the Medicare inpatient deductible. However, prolonged OS stays potentially increase this cost sharing.