bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase ordering of hard needles on a quasicrystalline substrate
Authors: Kählitz Philipp , Stark Holger
Published: May 2012

Quasicrystals possess long-range positional and orientational order. However, they cannot be periodic in space due to their non-crystallographic symmetries such as a 10-fold rotational axis. We perform Monte Carlo simulations of two-dimensional hard-needle systems subject to a quasiperiodic substrate potential. We determine phase diagrams as a function of density and potential strength for two needle lengths. With increasing potential strength short needles tend to form isolated clusters that display directional order along the decagonal directions. Long needles create interacting clusters that stabilize the nematic phase. At large potential strengths the clusters position themselves on two interwoven Fibonacci sequences perpendicular to the cluster orientation. Alternatively, one obtains extended domains of needle clusters which are aligned along all decagonal symmetry directions.
Nonlinear phonon transport and ballistic thermal rectification in asymmetric graphene-based three terminal junctions
Authors: Xie Zhong-Xiang , Li Ke-Min , Tang Li-Ming , Pan Chang-Ning , Chen Ke-Qiu
Published: May 2012

By using the nonequilibrium Green’s function and the Landauer transport theory, nonlinear phonon properties in asymmetric graphene-based three terminal junctions (AGTTJs) are investigated. Results show that AGTTJs exhibit pronounced nonlinear thermal rectifying behaviors, and the efficiency is efficiently tuned by increasing the asymmetric degree between the left and right terminals or modulating the central probe. The thermal rectifying mechanism is analytically explained by the schematic diagram. It is suggested that AGTTJs may be served as a good ballistic thermal rectifier.
Single mode phonon scattering at carbon nanotube-graphene junction in pillared graphene structure
Authors: Lee Jonghoon , Varshney Vikas , Brown Joshua S. , Roy Ajit K. , Farmer Barry L.
Published: May 2012

Phonon scattering at the carbon nanotube-graphene interface is studied in the pillared graphene structure, using the phonon wave packet method. Qualitatively different scattering characteristics, compared to previous studies of carbon nanotube systems, are observed. The phonon group velocity, dictating the energy transmission in simple carbon nanotube systems, is found to play an insignificant role. Distributing the incoming phonon energy to both sides of the interface more or less equally, the graphene interface provides a strong diffusive scattering site, which features a microscopic understanding of the decisive role of junction on the thermal transport in the pillared graphene hierarchical structure.
Tesla coil discharges guided by femtosecond laser filaments in air
Authors: Brelet Yohann , Houard Aurélien , Arantchouk Leonid , Forestier Benjamin , Liu Yi , Prade Bernard , Carbonnel Jérôme , André Yves-Bernard , Mysyrowicz André
Published: May 2012

A Tesla coil generator was designed to produce high voltage pulses oscillating at 100 kHz synchronisable with a nanosecond temporal jitter. Using this compact high voltage generator, we demonstrate reproducible meter long discharges in air at a repetition rate of 1 Hz. Triggering and guiding of the discharges are performed in air by femtosecond laser filaments.
Temperature dependence of frequency response characteristics in organic field-effect transistors
Authors: Lu Xubing , Minari Takeo , Liu Chuan , Kumatani Akichika , Liu J.-M. , Tsukagoshi Kazuhito
Published: May 2012

The frequency response characteristics of semiconductor devices play an essential role in the high-speed operation of electronic devices. We investigated the temperature dependence of dynamic characteristics in pentacene-based organic field-effect transistors and metal-insulator-semiconductor capacitors. As the temperature decreased, the capacitance-voltage characteristics showed large frequency dispersion and a negative shift in the flat-band voltage at high frequencies. The cutoff frequency shows Arrhenius-type temperature dependence with different activation energy values for various gate voltages. These phenomena demonstrate the effects of charge trapping on the frequency response characteristics, since decreased mobility prevents a fast charge response for alternating current signals at low temperatures.
New exact solutions for Hele-Shaw flow in doubly connected regions
Authors: Dallaston Michael C. , McCue Scott W.
Published: May 2012

Radial Hele–Shaw flows are treated analytically using conformal mapping techniques. The geometry of interest has a doubly connected annular region of viscous fluid surrounding an inviscid bubble that is either expanding or contracting due to a pressure difference caused by injection or suction of the inviscid fluid. The zero-surface-tension problem is ill-posed for both bubble expansion and contraction, as both scenarios involve viscous fluid displacing inviscid fluid. Exact solutions are derived by tracking the location of singularities and critical points in the analytic continuation of the mapping function. We show that by treating the critical points, it is easy to observe finite-time blow-up, and the evolution equations may be written in exact form using complex residues. We present solutions that start with cusps on one interface and end with cusps on the other, as well as solutions that have the bubble contracting to a point. For the latter solutions, the bubble approaches an ellipse in shape at extinction.
Maximum entropy states of quasi-geostrophic point vortices
Authors: Miyazaki Takeshi , Sato Tomoyoshi , Takahashi Naoya
Published: May 2012

The statistical equilibrium state of quasi-geostrophic point vortices is investigated theoretically, based on the maximum entropy theory. We search for the state of maximum Shannon entropy under the constraints of the vertical vorticity distribution P(z), the angular momentum I, and the energy of the vortex system E. Solutions of the mean field equation are obtained by the numerical procedure proposed by Turkington and Whittaker. The most probable state in an infinite fluid domain is axisymmetric, whose radial distribution depends both on the vertical vortex distribution P(z) and the total energy of the vortex system E. At a certain critical energy value Ec, the number of microscopic state of fixed angular momentum becomes largest (zero-inverse temperature state), where the radial distribution is Gaussian at any vertical height. When the energy is smaller (E < Ec: positive temperature), the radial distribution becomes flatter than the Gaussian. In contrast, if the energy is higher (E > Ec: negative temperature), the radial distribution becomes sharper showing tighter concentration near the axis of symmetry. In order to compare with these theoretical results, very long numerical computations are performed using the fast special-purpose computer for molecular dynamics simulations (GRAPE-DR). Quantitative agreements between the theoretical and numerical results are found for any cases considered.
Schottky barrier inhomogeneities at the interface of few layer epitaxial graphene and silicon carbide
Authors: Shivaraman Shriram , Herman Lihong H. , Rana Farhan , Park Jiwoong , Spencer Michael G.
Published: May 2012

In this work, we study electron transport across the heterojunction interface of epitaxial few-layer graphene grown on silicon carbide and the underlying substrate. The observed Schottky barrier is characterized using current-voltage, capacitance-voltage and photocurrent spectroscopy techniques. It is found that the graphene/SiC heterojunction cannot be characterized by a single unique barrier height because of lateral barrier inhomogeneities. A Gaussian distribution of barrier heights with a mean barrier height φBm=1.06eV and standard deviation σ=137±11meV explains the experimental data quite well.
Room temperature single GaN nanowire spin valves with FeCo/MgO tunnel contacts
Authors: Kum Hyun , Heo Junseok , Jahangir Shafat , Banerjee Animesh , Guo Wei , Bhattacharya Pallab
Published: May 2012

We report the direct measurement of spin transport characteristics in a GaN spin valve, with a relatively defect-free single GaN nanowire (NW) as the channel and FeCo/MgO as the tunnel barrier spin contact. Hanle spin precession and non-local transport measurements are made in an unintentionally doped nanowire spin valves. Spin diffusion length and spin lifetime values of 260 nm and 100 ps, respectively, are derived. Appropriate control measurements have been made to verify spin injection, transport, and detection.
Boldness behavior and stress physiology in a novel urban environment suggest rapid correlated evolutionary adaptation
Authors: Atwell Jonathan W. , Cardoso Gonçalo C. , Whittaker Danielle J. , Campbell-Nelson Samuel , Robertson Kyle W. , Ketterson Ellen D.
Published: May 2012

Novel or changing environments expose animals to diverse stressors that likely require coordinated hormonal and behavioral adaptations. Predicted adaptations to urban environments include attenuated physiological responses to stressors and bolder exploratory behaviors, but few studies to date have evaluated the impact of urban life on codivergence of these hormonal and behavioral traits in natural systems. Here, we demonstrate rapid adaptive shifts in both stress physiology and correlated boldness behaviors in a songbird, the dark-eyed junco, following its colonization of a novel urban environment. We compared elevation in corticosterone (CORT) in response to handling and flight initiation distances in birds from a recently established urban population in San Diego, California to birds from a nearby wildland population in the species' ancestral montane breeding range. We also measured CORT and exploratory behavior in birds raised from early life in a captive common garden study. We found persistent population differences for both reduced CORT responses and bolder exploratory behavior in birds from the colonist population, as well as significant negative covariation between maximum CORT and exploratory behavior. Although early developmental effects cannot be ruled out, these results suggest contemporary adaptive evolution of correlated hormonal and behavioral traits associated with colonization of an urban habitat.
A novel variational Bayes multiple locusZ-statistic for genome-wide association studies with Bayesian model averaging
Authors: Logsdon Benjamin A. , Carty Cara L. , Reiner Alexander P. , Dai James Y. , Kooperberg Charles
Published: May 2012

Motivation: For many complex traits, including height, the majority of variants identified by genome-wide association studies (GWAS) have small effects, leaving a significant proportion of the heritable variation unexplained. Although many penalized multiple regression methodologies have been proposed to increase the power to detect associations for complex genetic architectures, they generally lack mechanisms for false-positive control and diagnostics for model over-fitting. Our methodology is the first penalized multiple regression approach that explicitly controls Type I error rates and provide model over-fitting diagnostics through a novel normally distributed statistic defined for every marker within the GWAS, based on results from a variational Bayes spike regression algorithm.

Results: We compare the performance of our method to the lasso and single marker analysis on simulated data and demonstrate that our approach has superior performance in terms of power and Type I error control. In addition, using the Women's Health Initiative (WHI) SNP Health Association Resource (SHARe) GWAS of African-Americans, we show that our method has power to detect additional novel associations with body height. These findings replicate by reaching a stringent cutoff of marginal association in a larger cohort.

Availability: An R-package, including an implementation of our variational Bayes spike regression (vBsr) algorithm, is available at http://kooperberg.fhcrc.org/soft.html.

Contact:  blogsdon@fhcrc.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Two effective methods for correcting experimental high-throughput screening data
Authors: Dragiev Plamen , Nadon Robert , Makarenkov Vladimir
Published: May 2012

Motivation: Rapid advances in biomedical sciences and genetics have increased the pressure on drug development companies to promptly translate new knowledge into treatments for disease. Impelled by the demand and facilitated by technological progress, the number of compounds evaluated during the initial high-throughput screening (HTS) step of drug discovery process has steadily increased. As a highly automated large-scale process, HTS is prone to systematic error caused by various technological and environmental factors. A number of error correction methods have been designed to reduce the effect of systematic error in experimental HTS (Brideau et al., 2003; Carralot et al., 2012; Kevorkov and Makarenkov, 2005; Makarenkov et al., 2007; Malo et al., 2010). Despite their power to correct systematic error when it is present, the applicability of those methods in practice is limited by the fact that they can potentially introduce a bias when applied to unbiased data. We describe two new methods for eliminating systematic error from HTS data based on a prior knowledge of the error location. This information can be obtained using a specific version of the t-test or of the χ2 goodness-of-fit test as discussed in Dragiev et al. (2011). We will show that both new methods constitute an important improvement over the standard practice of not correcting for systematic error at all as well as over the B-score correction procedure (Brideau et al., 2003) which is widely used in the modern HTS. We will also suggest a more general data preprocessing framework where the new methods can be applied in combination with the Well Correction procedure (Makarenkov et al., 2007). Such a framework will allow for removing systematic biases affecting all plates of a given screen as well as those relative to some of its individual plates.

Contact:  makarenkov.vladimir@uqam.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization
Authors: Liao Yu-Chieh , Tsai Ming-Hsin , Chen Feng-Chi , Hsiung Chao A.
Published: May 2012

Motivation: Genome-scale metabolic network models have become an indispensable part of the increasingly important field of systems biology. Metabolic systems biology studies usually include three major components—network model construction, objective- and experiment-guided model editing and visualization, and simulation studies based mainly on flux balance analyses. Bioinformatics tools are required to facilitate these complicated analyses. Although some of the required functions have been served separately by existing tools, a free software resource that simultaneously serves the needs of the three major components is not yet available.

Results: Here we present a software platform, GEMSiRV (GEnome-scale Metabolic model Simulation, Reconstruction and Visualization), to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies. GEMSiRV comes with downloadable, ready-to-use public-domain metabolic models, reference metabolite/reaction databases and metabolic network maps, all of which can be input into GEMSiRV as the starting materials for network construction or simulation analyses. Furthermore, all of the GEMSiRV-generated metabolic models and analysis results, including projects in progress, can be easily exchanged in the research community. GEMSiRV is a powerful integrative resource that may facilitate the development of systems biology studies.

Availability: The software is freely available on the web at http://sb.nhri.org.tw/GEMSiRV.

Contact:  jade@nhri.org.tw
A holistic in silico approach to predict functional sites in protein structures
Authors: Segura Joan , Jones Pamela F. , Fernandez-Fuentes Narcis
Published: May 2012

Motivation: Proteins execute and coordinate cellular functions by interacting with other biomolecules. Among these interactions, protein–protein (including peptide-mediated), protein–DNA and protein–RNA interactions cover a wide range of critical processes and cellular functions. The functional characterization of proteins requires the description and mapping of functional biomolecular interactions and the identification and characterization of functional sites is an important step towards this end.

Results: We have developed a novel computational method, Multi-VORFFIP (MV), a tool to predicts protein-, peptide-, DNA- and RNA-binding sites in proteins. MV utilizes a wide range of structural, evolutionary, experimental and energy-based information that is integrated into a common probabilistic framework by means of a Random Forest ensemble classifier. While remaining competitive when compared with current methods, MV is a centralized resource for the prediction of functional sites and is interfaced by a powerful web application tailored to facilitate the use of the method and analysis of predictions to non-expert end-users.

Availability:  http://www.bioinsilico.org/MVORFFIP

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  naf4@aber.ac.uk; narcis.fernandez@gmail.com
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
Authors: Chen Ken , Wallis John W. , Kandoth Cyriac , Kalicki−Veizer Joelle M. , Mungall Karen L. , Mungall Andrew J. , Jones Steven J. , Marra Marco A. , Ley Timothy J. , Mardis Elaine R. , Wilson Richard K. , Weinstein John N. , Ding Li
Published: May 2012

Summary: Despite recent progress, computational tools that identify gene fusions from next-generation whole transcriptome sequencing data are often limited in accuracy and scalability. Here, we present a software package, BreakFusion that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency.

Availability:  http://bioinformatics.mdanderson.org/main/BreakFusion

Contact:  kchen3@mdanderson.org; lding@genome.wustl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online
Prevalence of preclinical and clinical heart failure in the elderly. A population‐based study in Central Italy
Authors: Mureddu Gian Francesco , Agabiti Nera , Rizzello Vittoria , Forastiere Francesco , Latini Roberto , Cesaroni Giulia , Masson Serge , Cacciatore Giuseppe , Colivicchi Furio , Uguccioni Massimo , Perucci Carlo Alberto , Boccanelli Alessandro ,   on behalf of the PREDICTOR Study Group
Published: May 2012

Aims

We conducted a population‐based cross‐sectional study to assess the prevalence of both preclinical and clinical heart failure (HF) in the elderly.

Methods and results

A sample of 2001 subjects, 65‐ to 84‐year‐old residents in the Lazio Region (Italy), underwent physical examination, biochemistry/N‐terminal pro brain natriuretic peptide (NT‐proBNP) assessment, electrocardiography, and echocardiography. Systolic left ventricular dysfunction (LVD) was defined as left ventricular ejection fraction (LVEF) <50%. Diastolic LVD was defined by a Doppler‐derived multiparametric algorithm. The overall prevalence of HF was 6.7% [95% confidence interval (CI) 5.6–7.9], mainly due to HF with preserved LVEF (HFpEF) (4.9%; 95% CI 4.0–5.9), and did not differ by gender. A systolic asymptomatic LVD (ALVD) was detected more frequently in men (1.8%; 95% CI 1.0–2.7) than in women (0.5%; 95% CI 0.1–1.0; P = 0.005), whereas the prevalence of diastolic ALVD was comparable between genders (men: 35.8%; 95% CI = 32.7–38.9; women: 35.0%; 95% CI = 31.9–38.2). The NT‐proBNP levels and severity of LVD increased with age. Overall, 1623 subjects (81.1% of the entire studied population) had preclinical HF (Stage A: 22.2% and stage B: 59.1% respectively). A large number of subjects in stage B of HF showed risk factor levels not at target.

Conclusions

In a population‐based study, the prevalence of preclinical HF in the elderly is high. The prevalence of clinical HF is mainly due to HFpEF and is similar between genders.
Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family

Sphingomonadaceae

, and reclassification of

Sphingomonas suberifaciens

as Sphingobium suberifaciens comb. nov.
Authors: Chen Hong , Jogler Mareike , Rohde Manfred , Klenk Hans-Peter , Busse Hans-Jürgen , Tindall Brian J. , Spröer Cathrin , Overmann Jörg
Published: May 2012

Two novel chemo-organoheterotrophic members of the

Sphingomonadaceae

were isolated from alpine and pre-alpine lakes. Cells stained Gram-negative, were motile and rod-shaped, and formed yellow, circular, convex colonies on different agar media. Strains 301T and 469T were strictly aerobic, catalase- and oxidase-positive, and grew at temperatures between 10 and 40 °C (optimum, 28 °C), and at pH values between 5 and 10 (optimum, pH 7). Both strains contained Q-10 as the dominant quinone, sphingoglycolipids and 2-hydroxymyristic acid, whereas 3-hydroxy fatty acids were absent. Major fatty acids of strain 301T were C18 : 1ω7c (53.3 %) and C16 : 1ω7c (22.9 %), with C14 : 0 2-OH (10.8 %) as the major 2-hydroxy fatty acid. Fatty acids of strain 469T were dominated by C18 : 1ω7c (34.4 %), C16 : 1ω7c (32.0 %) and C14 : 0 2-OH (15.2 %) as the major 2-hydroxy fatty acid. The genomic DNA G+C contents of strains 301T and 469T were 63.4 and 64.6 mol%, respectively. 16S rRNA gene sequence comparison indicated that both strains belonged to the genus

Sphingobium

. This classification was supported by the presence of spermidine as the major polyamine. The phylogenetically closest relatives of strain 301T were

Sphingobium amiense

DSM 16289T,

Sphingobium vermicomposti

DSM 21299T,

Sphingobium yanoikuyae

DSM 7462T and

Sphingobium scionense

DSM 19371T (98.8, 98.0, 97.9 and 97.4 % sequence similarity, respectively). DNA–DNA hybridization of genomic DNA yielded similarities in the range 43.2–12.1 % between strain 301T and the type strains of these four

Sphingobium

species. Closest relatives of strain 469T were

Sphingomonas suberifaciens

DSM 7465T and

Sphingobium scionense

DSM 19371T (97.1 and 96.5 % 16S rRNA gene sequence similarity, respectively). The degree of DNA–DNA hybridization between strain 469T and

Sphingomonas suberifaciens

DSM 7465T was 17.9 %. Based on the results of the molecular analyses and their phenotypic characteristics, strains 301T and 469T represent two novel species of the genus

Sphingobium

. The name Sphingobium limneticum sp. nov. is proposed for strain 301T( = DSM25076T = LMG 26659T). The name Sphingobium boeckii sp. nov. is proposed for strain 469T ( = DSM 25079T = LMG 26901T). The polyphasic analysis also suggests that

Sphingomonas suberifaciens

should be reclassified as Sphingobium suberifaciens comb. nov. with Ca1T ( = EY 2404T = ATCC 49355T = CIP 105429T = DSM 7465T = ICMP 12535T = NBRC 15211T = JCM 8521T = LMG 17323T = NCPPB 3629T) as the type strain.
Lacinutrix himadriensis sp. nov., a psychrophilic bacterium isolated from a marine sediment, and emended description of the genus

Lacinutrix
Authors: Srinivas T. N. R. , Prasad S. , Manasa P. , Sailaja B. , Begum Z. , Shivaji S.
Published: May 2012

A novel Gram-negative, rod-shaped, non-motile, psychrophilic bacterium, designated strain E4-9aT, was isolated from a marine sediment sample collected at a depth of 276 m from Kongsfjorden, Svalbard, in the Arctic Ocean. The colony colour was golden yellow. Strain E4-9aT was positive for amylase activity at 5 °C. The predominant fatty acids were iso-C15 : 1 G (21.8 %), anteiso-C15 : 0 (19.1 %), anteiso-C15 : 1 A (18.6 %), iso-C15 : 0 (13.8 %) and iso-C16 : 1 H (6.4 %). Strain E4-9aT contained MK-6 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids (AL1, AL4 and AL5), an unidentified phospholipid and four unidentified lipids (L1, L4 to L6). Based on 16S rRNA gene sequence similarity, it was ascertained that the closest related species to E4-9aT were

Lacinutrix copepodicola

,

L. algicola

and

L. mariniflava

, with sequence similarity to the respective type strains of 98.5, 96.5 and 95.8 %. Phylogenetic analysis showed that strain E4-9aT clustered with the type strain of

L. copepodicola

and with those of

L. algicola

and

L. mariniflava

at distances of 1.5 and 4.8 % (98.5 and 95.2 % similarity), respectively. However, DNA–DNA hybridization with

L. copepodicola

DJ3T showed 59 % relatedness with respect to strain E4-9aT. The DNA G+C content of strain E4-9aT was 29 mol%. Based on the results of DNA–DNA hybridization and phenotypic data, it appears that strain E4-9aT represents a novel species of the genus

Lacinutrix

, for which the name Lacinutrix himadriensis sp. nov. is proposed. The type strain is E4-9aT ( = CIP 110310T  = KCTC 23612T).
Methanothermobacter

tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field
Authors: Nakamura Kohei , Takahashi Azumi , Mori Chikahiro , Tamaki Hideyuki , Mochimaru Hanako , Nakamura Kazunori , Takamizawa Kazuhiro , Kamagata Yoichi
Published: May 2012

A thermophilic and hydrogenotrophic methanogen, strain RMAST, was isolated from gas-associated formation water of a gas-producing well in a natural gas field in Japan. Strain RMAST grew solely on H2/CO2 but required Casamino acids, tryptone, yeast extract or vitamins for growth. Growth of strain RMAST was stimulated by acetate. Cells were non-motile, straight rods (0.5×3.5–10.5 µm) and occurred singly or in pairs. Bundles of fimbriae occurred at both poles of cells and the cell wall was thick (approximately 21 nm, as revealed by ultrathin section electron microscopy). Strain RMAST grew at 45–80 °C (optimum, 70 °C), at pH 5.8–8.7 (optimum, pH 6.9–7.7) and with 0.001–20 g NaCl l−1 (optimum, 2.5 g NaCl l−1). Phylogenetic analysis revealed that

Methanothermobacter thermautotrophicus

ΔHT was most closely related to the isolate (95.7 % 16S rRNA gene sequence similarity). On the basis of morphological, phenotypic and phylogenetic characteristics, it is clear that strain RMAST represents a novel species of the genus

Methanothermobacter

, for which we propose the name

Methanothermobacter

tenebrarum sp. nov. The type strain is RMAST ( = DSM 23052T = JCM 16532T = NBRC 106236T).
HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies
Authors: Huang Shengfeng , Chen Zelin , Huang Guangrui , Yu Ting , Yang Ping , Li Jie , Fu Yonggui , Yuan Shaochun , Chen Shangwu , Xu Anlong
Published: May 2012

Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%–5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.
Mutation mapping and identification by whole-genome sequencing
Authors: Leshchiner Ignaty , Alexa Kristen , Kelsey Peter , Adzhubei Ivan , Austin-Tse Christina A. , Cooney Jeffrey D. , Anderson Heidi , King Matthew J. , Stottmann Rolf W. , Garnaas Maija K. , Ha Seungshin , Drummond Iain A. , Paw Barry H. , North Trista E. , Beier David R. , Goessling Wolfram , Sunyaev Shamil R.
Published: May 2012

Genetic mapping of mutations in model systems has facilitated the identification of genes contributing to fundamental biological processes including human diseases. However, this approach has historically required the prior characterization of informative markers. Here we report a fast and cost-effective method for genetic mapping using next-generation sequencing that combines single nucleotide polymorphism discovery, mutation localization, and potential identification of causal sequence variants. In contrast to prior approaches, we have developed a hidden Markov model to narrowly define the mutation area by inferring recombination breakpoints of chromosomes in the mutant pool. In addition, we created an interactive online software resource to facilitate automated analysis of sequencing data and demonstrate its utility in the zebrafish and mouse models. Our novel methodology and online tools will make next-generation sequencing an easily applicable resource for mutation mapping in all model systems.
Microeconomic impacts of a state‐funded farmer loan program
Authors: Pederson Glenn , Chung Wonho , Nel Roelof
Published: May 2012

Purpose

The purpose of this paper is to determine if there are positive microeconomic effects from a state‐funded loan participation program on farm productivity and investment behavior.

Design/methodology/approach

The authors take the approach that access to credit solves a liquidity problem. If a credit constraint exists it results in a suboptimal allocation of resources and a reduction in farm output and profitability. A two‐stage regression model approach is used to analyze farmer survey and loan application data. In the first stage, a probit regression model is used to identify the farmers who are likely to be credit rationed. In the second stage, switching regression models are used to observe the effect of credit rationing on farm productivity and on farm investment behavior.

Findings

It is found that there are liquidity effects of credit constraints for a significant share of the beginning and low‐resource farmers who participated in the state‐funded farm loan program. After controlling for various farm and farmer characteristics, the estimated productivity and investment demand equations imply that a 1 percent increase in credit received by credit constrained farmers under the state program increased their gross income by about 0.49 percent, and their investments in depreciable assets by about 0.33 percent.

Originality/value

This paper is the first to apply the switching regression model to a state‐funded farm loan program for the purpose of evaluating the financial impacts on farmer participants.
Land registration, credit and agricultural investment in Africa
Authors: Domeher Daniel , Abdulai Raymond
Published: May 2012

Purpose

The purpose of this paper is to critically examine the argument linking land registration to agricultural investment and to provide theoretical reasons as to why this linkage may not materialise in Africa within the short to medium term.

Design/methodology/approach

The paper takes the form of a critical review of the relevant literature on land registration, access to credit and agricultural investment; arguments are built on empirical studies found in the literature and theoretical concepts.

Findings

It has been established in this paper that the links between landed property registration and agricultural investments are made defective in Africa by factors such as poverty, lack of appropriate agro‐based infrastructure and the fact that land registrationper sedoes not improve the profitability of agriculture, neither does it improve access to credit.

Research limitations/implications

The fact that this paper is based on literature review may be seen as a weakness to some extent.

Originality/value

Even though previous researchers have looked at the relationship between landed property registration and agricultural investment in the developing world, they fall short of critically explaining why land registration has been found not to enhance agricultural investment. This paper fills the gap through a combination of various theoretical and practical arguments which could call for a rethinking on the policies for promoting agricultural growth. The rigorous theoretical argument may also provide the basis for further empirical research.
Implications of within county yield heterogeneity for modeling crop insurance premiums
Authors: Cooper Joseph , Zulauf Carl , Langemeier Michael , Schnitkey Gary
Published: May 2012

Purpose

Farm level data are essential to accurate setting of crop insurance premium rates, but their time series tends to be too short to allow them to be the sole data source. County level data are available in longer time series, however. The purpose of this paper is to present a methodology to make full use of the information inherent in each of these data sets.

Design/methodology/approach

The paper uses a novel application of statistical tools for using farm and county level yield data to generate farm level yield densities that explicitly incorporate within county yield heterogeneity while accounting for systemic risk and other spatial or intertemporal correlations among farms within the county.

Findings

The empirical analysis shows that current approaches used by the Risk Management Agency to individualize premiums for a farm result in substantial mispricing of crop insurance premiums because they do not adequately capture farm yield variability and yield correlations between farms. The new premium setting method is empirically shown to substantially reduce government subsidies for crop insurance premiums.

Originality/value

The paper demonstrates how to extract more information from available data when setting crop insurance premiums, which allows the government to more closely tailor premiums to the farm than do current approaches.
Development process of organic and local food breakfasts
Authors: Tikkanen Irma , Kasurinen Antero
Published: May 2012

Purpose

This paper aims to describe the development process of two organic and local food breakfasts to be served in a small and independent coffee shop in Finland.

Design/methodology/approach

A conceptual framework is established concerning corporate social responsibility (CSR) and new product development process. Previous research related to organic food, local food, and breakfasts is introduced. Action research is applied.

Findings

Two organic and local food breakfasts were developed as a process and sold during eight months in the case coffee shop. The process comprised nine stages. The components for the two breakfasts were received from nine suppliers.

Practical implications

The practical implications on the case coffee shop are that the customers' requests on organic and local food breakfasts were met; the coffee shop improved its sales and profits; and the service concept was moved into a more sustainable direction. The implications on the local society are that the sales of organic and local food producers increased and their employment improved.

Originality/value

Two organic and local food breakfasts were developed based on the product development process. The developed breakfasts can be used as a reference model in coffee shops, in restaurants, and in teaching.
Value net – a new business model for the food industry?
Authors: Kähkönen Anni‐Kaisa
Published: May 2012

Purpose

The study aims to discuss the new value creation logic of value nets and analyze the characteristics of value nets in the context of the food industry. Previous research has shown that along with the growing importance of networking, the value creation logic is also changing from traditional chains to dynamic networks. The objective of this study is to define the characteristics of value nets and to analyze the suitability of the value net as a value creation and business model in the food industry.

Design/methodology/approach

The study utilizes a case research as a method and analyzes a value net from the Finnish food industry. The empirical data comprises 29 individual semi‐structured interviews conducted with the personnel of four case companies.

Findings

The findings of the study suggest that the value net as a business model and value creation model is also suitable for food sector companies. The value net has several characteristics that were found to be significant and useful for food companies. Moreover, food companies can obtain remarkable benefits by utilizing value nets.

Practical implications

The results of the study carry implications for managers and practitioners in terms of shedding light on the value net as a value creation model and business model in the food industry. Managers need to be aware of the developments in value creation logic and recognize that value can no longer be added in a sequential chain, but the perspective should move towards networks in which value is co‐created by the network actors.

Originality/value

Thus far, studies on value nets have concentrated mainly on the ICT sector and there is a limited amount of research on the food industry. The food sector, therefore, offers a new empirical context in which to conduct research on value nets. Food companies are focusing more and more on value creation and networking, and the research of value nets is therefore highly relevant to the business development of the food industry.
The effects of social‐economic status of consumers on purchasing, behaving and attitude to food products
Authors: Koç Beşir , Ceylan Melike
Published: May 2012

Purpose

The aim of the study is to group consumers according to their own perception of socio‐economic status and to determine consumption habits, behaviors, approach and tendency towards food products.

Design/methodology/approach

In this study, consumers in urban areas of Van, in Turkey, were grouped according to their self‐perceived social‐economic status and their behaviors and attitudes on purchase of food products are examined according to that social‐economic status. The study was conducted in Van province, Turkey, during 2007‐2008. Face to face interviews with 300 consumers work through the survey data was collected. Participants were asked to indicate their socio‐economic status from a choice of top, middle and bottom level groups.

Findings

Within the top and middle level of this grouping, the percentage of high school graduates is high; at the bottom level of this status, the proportion of university graduates is high. A large percentage of the consumers are public servants and business owners. It was observed that as the socio‐economic status increased, the proportion of business owners increased as well. Consumers in lower status groups spend the biggest portion of their income on food products. As the wages increase, the level of spending on food product decreases proportionally and the ability to make savings increases. The highest status consumers always check the price labels of the food products with a high percentage (66.67 percent). More than half of consumers do not believe that producers write all information and ingredients of the products on the packaging. A total of 77 percent of study participants stated that they were open to trying new food products. Consumers within the top socio‐economic groups are most careful about food ingredients.

Originality/value

In this study, the consumers themselves are classified according to their socio‐economic status. These are the top, middle and bottom status as determined. Consumers are clustered according to the general characteristics of the correspondence analysis.
Increasing the competitive positions of countries through employee training
Authors: Yan Cheung Hoi , Chan Alex W.H.
Published: May 2012

Purpose

The purpose of this paper is to look at the competitiveness motive and mastery motive across 33 countries. The competitiveness motive is found to be a significant but negative predictor of employee training.

Design/methodology/approach

The dataset was collected from two sources. Competitiveness motive and mastery motive scores of countries were collected from Lynn's study (1991); and work relation variables, such as employee training, worker motivation, and the world competitiveness score, were collected from the IMD World Competitiveness Yearbook 2008. Correlations, regression models and Sobel test were applied for analysis.

Findings

Although people with a strong competitiveness motive are eager to beat others, the results indicate that they may not see training as an effective method of beating others in terms of the competitiveness positions of their country. Employee training is found to be related to the work motivation of employees, and thus to the competitiveness positions of countries. Some suggestions are made for such outcomes.

Practical implications

The paper highlights the importance of employee training in organizations.

Originality/value

The paper demonstrates the importance of training with regard to global competitiveness positions.
Write‐in comments in employee surveys
Authors: Borg Ingwer , Zuell Cornelia
Published: May 2012

Purpose

Items that ask the respondent for a comment in his/her own words are becoming increasingly popular in online employee surveys, but research on such comments is scarce. The purpose of this paper is to analyze, theoretically and empirically, what kind of comments are generated in employee surveys by respondents who differ in terms of job satisfaction and commitment.

Design/methodology/approach

The data studied here are from an online employee survey conducted in 2004 in a multinational IT organization with a German headquarter. Some 24,000 employees generated about 75,000 comments focusing on 15 topic fields. The comments were additionally coded on their tone, using a computerized dictionary approach especially developed for this purpose. Frequencies, wordiness, and the tone of different types of comments are measured. The statistical relationship of comments to job satisfaction and to organizational commitment is analyzed.

Findings

Some 40 per cent of the respondents provide comments. Most comments have a negative tone. Negative comments are wordier than positive ones. The likelihood of writing comments is inversely related to the respondents’ job satisfaction and to their organizational commitment. Dissatisfied employees and employees with low commitment also write more negative and wordier comments.

Practical implications

The study sets benchmarks on what to expect when using open‐ended comment fields in employee surveys. A methodology for analyzing huge text files with respect to their tone is presented.

Originality/value

This is the first paper that investigates a realistically large data set of comments. It also shows how to use computer methods to relate frequencies, wordiness, and tone of comments to standard variables such as job satisfaction or commitment.
The impact of internal and external market orientation on performance in local public organisations
Authors: Rodrigues Ana Paula , Carlos Pinho José
Published: May 2012

Purpose

This study aims to build on and extend the literature of market orientation by examining the impact of sub‐dimensions of both internal and external market orientation on financial and non‐financial performance in the local public sector context.

Design/methodology/approach

In line with previous studies on market orientation, a quantitative research design was adopted. The data collection was performed through a mail survey of a sample of local Portuguese public organisations (municipality executive board members). Structural equation modelling was used as a means to analyse the hypothesised relationships.

Findings

Six out of 12 hypotheses are supported. Concerning the sub‐components of external market orientation, the study finds that the dissemination and responsiveness of external information impacts strongly on non‐financial performance. In turn, external information generation and responsiveness impacts positively on financial performance. With respect to internal market orientation, results revealed a lower impact of different sub‐dimensions on performance. Specifically, the only dimension that impacts positively on organisational performance (financial and non‐financial) is internal information generation. This reinforces the view that there is a need to strengthen internal information dissemination and responsiveness to enhance organisational performance.

Originality/value

This paper offers original and unique findings and to the best of the authors' knowledge this research is one of the few studies addressing the role of internal and external sub‐dimensions of market orientation on performance in the local public sector. The findings of this study add weight to the recent emphasis on disaggregate approaches to (internal and external) market orientation‐performance link.
Can after sale service generate brand equity?
Authors: Ahmad Sajjad , Mohsin Butt Muhammad
Published: May 2012

Purpose

This research attempts to empirically expand the Aaker's consumer based brand equity model in hybrid business firms by incorporating after sales service as a new dimension. Exploring and understanding the drivers of consumer based brand equity in a hybrid business context will help in building industry specific competitive barriers and generating brand wealth.

Design/methodology/approach

The data were collected from Pakistani adults using a structured questionnaire based on established scales. Convenience sampling was used to gather data from 205 respondents across the major cities of Pakistan. To test the proposed research model the data were analyzed using confirmatory factor analysis.

Findings

The results support the proposed five‐factor model of consumer based brand equity for the automotive industry. The results support the notion that after sales service is related but is a separate dimension of consumer based brand equity in the automotive sector.

Research limitations/implications

This proposed CBBE model was tested in the automotive sector of Pakistan. However, the automotive industry is special in the sense that it builds brands at dual level. This study only investigates consumer based brand equity at marque level. Future studies can expand on this work by investigating consumer based brand equity both at marque and model levels.

Practical implications

The establishment of after sale services as a separate but independent dimension of consumer based brand equity for the hybrid business organizations provides a fresh reminder regarding the possibilities of new sources for building brand equity. Managers can focus on delivering excellent after sale services to build and enhance the equity of their brands in hybrid business organizations.

Originality/value

This study expands Aaker's brand equity model by empirically establishing after sales service as a fifth dimension for the firms operating on hybrid business model.