bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predation and protists
Authors: Kirchman David L. 
Published: December 2013

Abstract
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

Abstract
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

AbstractAn 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

Abstract
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

Abstract
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

Abstract
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

Abstract

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.
An Adaptive Threshold in Mammalian Neocortical Evolution
Authors: Lewitus Eric , Kelava Iva , Kalinka Alex T. , Tomancak Pavel , Huttner Wieland B 
Published: December 2013

AbstractExpansion 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)
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

Abstract
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

Abstract
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.