bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling of genetic interactions improves prediction of hybrid patterns – a case study in domestic fowl
Authors: ÁLVAREZ-CASTRO JOSÉ M. , LE ROUZIC ARNAUD , ANDERSSON LEIF , SIEGEL PAUL B. , CARLBORG ÖRJAN 
Published: January 2013

SummaryA major challenge in complex trait genetics is to unravel how multiple loci and environmental factors together cause phenotypic diversity. Both first (F1) and second (F2) generation hybrids often display phenotypes that deviate from what is expected under intermediate inheritance. We have here studied two chicken F2populations generated by crossing divergent chicken lines to assess how epistatic loci, identified in earlier quantitative trait locus (QTL) studies, contribute to hybrid deviations from the mid-parent phenotype. Empirical evidence suggests that the average phenotypes of the intercross birds tend to be lower than the midpoint between the parental means in both crosses. Our results confirm that epistatic interactions, despite a relatively small contribution to the phenotypic variance, play an important role in the deviation of hybrid phenotypes from the mid-parent values (i.e. multi-locus hybrid genotypes lead to lower rather than higher body weights). To a lesser extent, dominance also appears to contribute to the mid-parent deviation, at least in one of the crosses. This observation coincides with the hypothesis that hybridization tends to break up co-adapted gene complexes, i.e. generate Bateson–Dobzhansky–Muller incompatibilities.
Degree of fetal growth restriction associated with schizophrenia risk in a national cohort
Authors: Eide M. G. , Moster D. , Irgens L. M. , Reichborn-Kjennerud T. , Stoltenberg C. , Skjærven R. , Susser E. , Abel K. 
Published: January 2013

BackgroundAccumulating evidence suggests that fetal growth restriction may increase risk of later schizophrenia but this issue has not been addressed directly in previous studies. We examined whether the degree of fetal growth restriction was linearly related to risk of schizophrenia, and also whether maternal pre-eclampsia, associated with both placental dysfunction and poor fetal growth, was related to risk of schizophrenia.MethodA population-based cohort of single live births in the Medical Birth Registry of Norway (MBRN) between 1967 and 1982 was followed to adulthood (n = 873 612). The outcome was schizophrenia (n=2207) registered in the National Insurance Scheme (NIS). The degree of growth restriction was assessed by computing sex-specific z scores (standard deviation units) of ‘birth weight for gestational age’ and ‘birth length for gestational age’. Analyses were adjusted for potential confounders. Maternal pre-eclampsia was recorded in the Medical Birth Registry by midwives or obstetricians using strictly defined criteria.ResultsThe odds ratio (OR) for schizophrenia increased linearly with decreasing birth weight for gestational age z scores (p value for trend = 0.005). Compared with the reference group (z scores 0.01–1.00), the adjusted OR [95% confidence interval (CI)] for the lowest z-score category (< − 3.00) was 2.0 (95% CI 1.2–3.5). A similar pattern was observed for birth length for gestational age z scores. Forty-nine individuals with schizophrenia were identified among 15 622 births with pre-eclampsia. The adjusted OR for schizophrenia following maternal pre-eclampsia was 1.3 (95% CI 1.0–1.8).ConclusionsAssociations of schizophrenia risk with degree of fetal growth restriction and pre-eclampsia suggest future research into schizophrenia etiology focusing on mechanisms that influence fetal growth, including placental function.
Differential patterns of activity and functional connectivity in emotion processing neural circuitry to angry and happy faces in adolescents with and without suicide attempt
Authors: Pan L. A. , Hassel S. , Segreti A. M. , Nau S. A. , Brent D. A. , Phillips M. L. 
Published: January 2013

BackgroundNeural substrates of emotion dysregulation in adolescent suicide attempters remain unexamined.MethodWe used functional magnetic resonance imaging to measure neural activity to neutral, mild or intense (i.e. 0%, 50% or 100% intensity) emotion face morphs in two separate emotion-processing runs (angry and happy) in three adolescent groups: (1) history of suicide attempt and depression (ATT, n = 14); (2) history of depression alone (NAT, n = 15); and (3) healthy controls (HC, n = 15). Post-hoc analyses were conducted on interactions from 3 group × 3 condition (intensities) whole-brain analyses (p < 0.05, corrected) for each emotion run.ResultsTo 50% intensity angry faces, ATT showed significantly greater activity than NAT in anterior cingulate gyral–dorsolateral prefrontal cortical attentional control circuitry, primary sensory and temporal cortices; and significantly greater activity than HC in the primary sensory cortex, while NAT had significantly lower activity than HC in the anterior cingulate gyrus and ventromedial prefrontal cortex. To neutral faces during the angry emotion-processing run, ATT had significantly lower activity than NAT in the fusiform gyrus. ATT also showed significantly lower activity than HC to 100% intensity happy faces in the primary sensory cortex, and to neutral faces in the happy run in the anterior cingulate and left medial frontal gyri (all p < 0.006,corrected). Psychophysiological interaction analyses revealed significantly reduced anterior cingulate gyral–insula functional connectivity to 50% intensity angry faces in ATT v. NAT or HC.ConclusionsElevated activity in attention control circuitry, and reduced anterior cingulate gyral–insula functional connectivity, to 50% intensity angry faces in ATT than other groups suggest that ATT may show inefficient recruitment of attentional control neural circuitry when regulating attention to mild intensity angry faces, which may represent a potential biological marker for suicide risk.
Modulation of extracellular d-serine content by calcium permeable AMPA receptors in rat medial prefrontal cortex as revealed by in vivo microdialysis
Authors: Ishiwata Sayuri , Umino Asami , Umino Masakazu , Yorita Kazuko , Fukui Kiyoshi , Nishikawa Toru 
Published: January 2013

Abstract
In mammalian brains, d-serine has been shown to be required for the regulation of glutamate neurotransmission as an endogenous co-agonist for the N-methyl-d-aspartate type glutamate receptor that is essential for the expression of higher-order brain functions. The exact control mechanisms for the extracellular d-serine dynamics, however, await further elucidation. To obtain an insight into this issue, we have characterized the effects of agents acting at the α-amino-3-hydroxy-5-methyl-4-isoxazolepropioinic acid (AMPA) type glutamate receptor on the extracellular d-serine contents in the medial prefrontal cortex of freely moving rats by an in vivo microdialysis technique in combination with high-performance liquid chromatography with fluorometric detection. In vivo experiments are needed in terms of a crucial role of d-serine in the neuron-glia communications despite the previous in vitro studies on AMPA receptor-d-serine interactions using the separated preparations of neurons or glial cells. Here, we show that the intra-cortical infusion of (S)-AMPA, an active enantiomer at the AMPA receptor, causes a significant and concentration-dependent reduction in the prefrontal extracellular contents of d-serine, which is reversed by an AMPA/kainate receptor antagonist, 2,3-dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[f]quinoxaline-7-sulfonamide disodium salt, and a calcium permeable AMPA receptor antagonist, 1-naphthyl acetyl spermine. The d-serine reducing effects of (S)-AMPA are augmented by co-infusion of cyclothiazide that prevents AMPA receptor desensitization. Our data support the view that a calcium permeable AMPA receptor subtype may exert a phasic inhibitory control on the extracellular d-serine release in the mammalian prefrontal cortex in vivo.
To Free or Not to Free? State Obligations and the Rescue and Release of Marine Mammals: A Case Study of ‘Morgan the Orca’
Authors: Trouwborst Arie , Caddell Richard , Couzens Ed 
Published: January 2013

AbstractWild animals periodically encounter difficulties or suffer injuries that require human intervention and assistance. The natural assumption is that a surviving animal will, where viable, be released back to the wild. But is there a formal legal obligation for a rescuer to do so? This question arose recently in the context of ‘Morgan’, a female killer whale rescued in poor health in Dutch waters. Morgan was successfully restored to full health, but the Dutch authorities subsequently declined to repatriate her to the wild and, controversially, transferred her to a zoological facility in Spain. This article examines the largely unexplored legal obligations incumbent upon the Netherlands in respect of rehabilitated cetaceans, in the process exposing certain problems of clarity and consistency within the present regulatory framework. By necessary implication, this article identifies emerging issues of interpretation posed by the Morgan saga, illustrating the tensions between animal welfare and nature conservation – especially in the transboundary context – and concluding firmly that the Dutch authorities erred legally in making their final decision.
Sampling Efficiency of the Moore Egg Collector
Authors: Worthington Thomas A. , Brewer Shannon K. , Grabowski Timothy B. , Mueller Julia 
Published: January 2013

Abstract
Quantitative studies focusing on the collection of semibuoyant fish eggs, which are associated with a pelagic broadcast-spawning reproductive strategy, are often conducted to evaluate reproductive success. Many of the fishes in this reproductive guild have suffered significant reductions in range and abundance. However, the efficiency of the sampling gear used to evaluate reproduction is often unknown and renders interpretation of the data from these studies difficult. Our objective was to assess the efficiency of a modified Moore egg collector (MEC) using field and laboratory trials. Gear efficiency was assessed by releasing a known quantity of gellan beads with a specific gravity similar to that of eggs from representatives of this reproductive guild (e.g., the Arkansas River Shiner Notropis girardi) into an outdoor flume and recording recaptures. We also used field trials to determine how discharge and release location influenced gear efficiency given current methodological approaches. The flume trials indicated that gear efficiency ranged between 0.0% and 9.5% (n = 57) in a simple 1.83-m-wide channel and was positively related to discharge. Efficiency in the field trials was lower, ranging between 0.0% and 3.6%, and was negatively related to bead release distance from the MEC and discharge. The flume trials indicated that the gellan beads were not distributed uniformly across the channel, although aggregation was reduced at higher discharges. This clustering of passively drifting particles should be considered when selecting placement sites for an MEC; further, the use of multiple devices may be warranted in channels with multiple areas of concentrated flow.
Received August 8, 2012; accepted October 12, 2012
A comprehensive SNP and indel imputability database
Authors: Duan Qing , Liu Eric Yi , Croteau-Chonka Damien C. , Mohlke Karen L. , Li Yun 
Published: January 2013

Abstract
Motivation: Genotype imputation has become an indispensible step in genome-wide association studies (GWAS). Imputation accuracy, directly influencing downstream analysis, has shown to be improved using re-sequencing-based reference panels; however, this comes at the cost of high computational burden due to the huge number of potentially imputable markers (tens of millions) discovered through sequencing a large number of individuals. Therefore, there is an increasing need for access to imputation quality information without actually conducting imputation. To facilitate this process, we have established a publicly available SNP and indel imputability database, aiming to provide direct access to imputation accuracy information for markers identified by the 1000 Genomes Project across four major populations and covering multiple GWAS genotyping platforms.
Results: SNP and indel imputability information can be retrieved through a user-friendly interface by providing the ID(s) of the desired variant(s) or by specifying the desired genomic region. The query results can be refined by selecting relevant GWAS genotyping platform(s). This is the first database providing variant imputability information specific to each continental group and to each genotyping platform. In Filipino individuals from the Cebu Longitudinal Health and Nutrition Survey, our database can achieve an area under the receiver-operating characteristic curve of 0.97, 0.91, 0.88 and 0.79 for markers with minor allele frequency &gt;5%, 3–5%, 1–3% and 0.5–1%, respectively. Specifically, by filtering out 48.6% of markers (corresponding to a reduction of up to 48.6% in computational costs for actual imputation) based on the imputability information in our database, we can remove 77%, 58%, 51% and 42% of the poorly imputed markers at the cost of only 0.3%, 0.8%, 1.5% and 4.6% of the well-imputed markers with minor allele frequency &gt;5%, 3–5%, 1–3% and 0.5–1%, respectively.
Availability: http://www.unc.edu/∼yunmli/imputability.html
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: yunli@med.unc.edu
GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process
Authors: Antoniotti Marco , Bader Gary D. , Caravagna Giulio , Crippa Silvia , Graudenzi Alex , Mauri Giancarlo 
Published: January 2013

Abstract
Summary: The characterization of the complex phenomenon of cell differentiation is a key goal of both systems and computational biology. GeStoDifferent is a Cytoscape plugin aimed at the generation and the identification of gene regulatory networks (GRNs) describing an arbitrary stochastic cell differentiation process. The (dynamical) model adopted to describe general GRNs is that of noisy random Boolean networks (NRBNs), with a specific focus on their emergent dynamical behavior. GeStoDifferent explores the space of GRNs by filtering the NRBN instances inconsistent with a stochastic lineage differentiation tree representing the cell lineages that can be obtained by following the fate of a stem cell descendant. Matched networks can then be analyzed by Cytoscape network analysis algorithms or, for instance, used to define (multiscale) models of cellular dynamics.
Availability: Freely available at http://bimib.disco.unimib.it/index.php/Retronet#GESTODifferent or at the Cytoscape App Store http://apps.cytoscape.org/.
Contact: marco.antoniotti@unimib.it
KEGGParser: parsing and editing KEGG pathway maps in Matlab
Authors: Arakelyan Arsen , Nersisyan Lilit 
Published: January 2013

Abstract
Summary: KEGG pathway database is a collection of manually drawn pathway maps accompanied with KGML format files intended for use in automatic analysis. KGML files, however, do not contain the required information for complete reproduction of all the events indicated in the static image of a pathway map. Several parsers and editors of KEGG pathways exist for processing KGML files. We introduce KEGGParser—a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment. It also works with Scilab.
Availability and implementation: The source code is available at http://www.mathworks.com/matlabcentral/fileexchange/37561.
Contact: aarakelyan@sci.am
Supplementary information: Supplementary data are available at Bioinformatics online.
Moderate turbidity enhances schooling behaviour in fish larvae in coastal waters
Authors: Ohata Ryosuke , Masuda Reiji , Takahashi Kohji , Yamashita Yoh 
Published: January 2013

AbstractWe evaluated the effects of turbidity on school formation in ayu (Plecoglossus altivelis) [24.5 ± 2.2 mm standard length (Ls)], Japanese anchovy (Engraulis japonicus) (29.1 ± 3.1 mm Ls) larvae, which often live in turbid coastal waters, and yellowtail (Seriola quinqueradiata) juveniles (37.1 ± 2.5 mm Ls), which live in clear offshore waters. Fish were introduced into experimental tanks at one of five turbidity levels obtained by dissolving 0, 5, 20, 50, or 300 mg l−1 of kaolin in seawater. Their behaviour was video recorded, and the nearest neighbour distance (DNN) and separation angle (AS) were compared among turbidity levels. Mean DNN of ayu was significantly smaller at 20 and 50 mg l−1 than any other level of turbidity, as was AS at 20 mg l−1 compared with 0 mg l−1. Mean AS of anchovy was smaller at 50 mg l−1 of turbidity than any others. In contrast, mean DNN of yellowtail was larger at 300 mg l−1 than any others. These results suggest that moderate turbidities enhance schooling behaviour in ayu and Japanese anchovy larvae, whereas turbidity has an inhibitive effect on schooling of yellowtail juveniles, corresponding well to the habitat characteristics of each species.
PS1-10jh – a tidal disruption event with an extremely low disc temperature
Authors: Armijo Matias Montesinos , de Freitas Pacheco J. A. 
Published: January 2013

Abstract
The cooler than expected optical–UV transient PS1-10jh detected by the Pan-STARRS1 survey is probably related to a tidal disruption event in which a He-rich stellar core remnant is implied. The evolution of bound debris during the disc-phase is studied by solving the hydrodynamic equations. The model provides a good fit either of the raising part of the light curve in the bands gP1, rP1 and iP1 or in the early decay. The parameters characterizing this optimized model are the mass of the central black hole, i.e. 6.3 × 106 M⊙, and the critical Reynolds number ${\cal R} = 10^4$ that fixes the viscosity and the accretion time-scale. Such a high value of ${\cal R}$ explains the low disc temperature and the consequent absence of X-ray emission. The predicted bolometric peak luminosity is about 1045 erg s− 1 and the predicted total radiated energy is about Erad = 2.67 × 1051 erg.
HIGH-PENETRATION OPTICAL COHERENCE TOMOGRAPHY AND ENHANCED DEPTH IMAGING IN PRESUMED RETINAL PIGMENT EPITHELIAL HAMARTOMA
Authors: Takahashi Ayako , Ooto Sotaro , Yoshimura Nagahisa 
Published: January 2013

Purpose:
To report on high-penetrating swept source optical coherence tomography (SS-OCT) imaging and enhanced depth imaging in an eye with presumed retinal pigment epithelial hamartoma .

Methods and Patients:
A 60-year-old man with presumed retinal pigment epithelial hamartoma underwent complete ophthalmologic examination, including fluorescein angiography, indocyanine green angiography, enhanced depth imaging OCT, and SS-OCT.

Results:
In the left eye, there were six darkly pigmented, nodular, circumscribed lesions in the macular area. The margins were well defined and were not associated with changes such as edema, exudation, or hemorrhage. Fluorescein angiography revealed a minimally dilated feeding artery and draining vein in each lesion. Spectral domain OCT demonstrated an elevation of the retina at the site of the lesions with greatly enhanced optical reflectivity of the inner surface and complete shadowing of optical transmission with crisp vertical margins. However, enhanced depth imaging OCT and SS-OCT revealed deeper retinal layer structures in the pigmented lesions. Intraretinal lesions showed superficial involvement and preretinal extension with or without superficial hyporeflective regions.

Conclusion:
Enhanced depth imaging OCT and SS-OCT revealed deeper retinal layer structures in the pigmented lesions in a case with presumed retinal pigment epithelial hamartoma. Enhanced depth imaging OCT and SS-OCT are useful for visualization of intraretinal structures in these lesions, leading to further investigation of the origin and development of retinal pigment epithelial hamartoma.
Capturing zero‐trade values in gravity equations of trade: an analysis of protectionism in agro‐food sectors
Authors: Philippidis George , Resano‐Ezcaray Helena , Sanjuán‐López Ana I. 
Published: January 2013

AbstractWith significant improvements in its theoretical underpinnings, the gravity model has gained renewed interest in the agro‐food trade literature. Notwithstanding, there is a dearth of literature examining the relative trade restrictiveness of tariff barriers across a broad range of agro‐food sectors. This represents an important research gap, which this study sets out to fill. Furthermore, this research reconciles the application of zero‐inflated models with a sectorally disaggregated analysis. More specifically, employing a fully specified gravity equation, a Poisson estimator and variants of the Poisson model (Negative Binomial, Zero‐Inflated Poisson, and Zero‐Inflated Negative Binomial) provide statistically significant and theoretically consistent estimates, while allowing for the inclusion of zero‐trade values. A panel data model with fixed effects is also employed to improve the estimation of the parameters of interest. Estimation results reveal that in the vast majority of sectors examined, import tariffs are found to be statistically significant, whereas export refunds exhibit a statistically smaller role due to the nonsystematic nature of their application in world food markets. Model simulations of tariff barrier eliminations reveal limited trade gains, although there is encouraging evidence of “low” and “lower middle” per capita income country trade gains in wheat, red meat, dairy, sugar, and (particularly) rice markets.
Expression and significance of Rac1, Pak1 and Rock1 in gastric carcinoma
Authors: Wu Yong‐jun , Tang Yi , Li Zhen‐feng , Li Zheng , Zhao Yi , Wu Zhen‐jiang , Su Qi 
Published: January 2013

AbstractAimsRac1, Pak1 and Rock1 are indicators related to gastric cancer invasion and metastasis, but few reports discuss all three kinds of protein in research on gastric cancer invasion and metastasis. The aim of this study was to investigate the expression and clinical significance of Rac1, Pak1 and Rock1 in gastric carcinoma.MethodsRac1, Pak1 and Rock1 expression in 158 cases of gastric carcinoma were investigated via immunohistochemical staining and clinical analysis.ResultsThe positive expression rates of Rac1, Pak1 and Rock1 in normal tissue, intraepithelial neoplastic tissues and gastric carcinoma showed an increasing trend (P < 0.05). Their expression in lymph node metastasis was significantly higher than in patients with lymph‐node metastasis than in those without lymph nodes metastasis (P < 0.05). Their expression in tumor (TNM stages III and IV) were significantly higher than that in stages I and II (P < 0.05). Rac1, Pak1 and Rock1 expression did not differ significantly with patients' sex (P > 0.05).ConclusionPositive rates of Rac1, Pak1 and Rock1 expression in normal tissue, dysplasia and gastric carcinoma show an increasing trend and are correlated with tumor lymph node metastasis and TNM stage. Rac1, Pak1 and Rock1 may be important biomarkers of gastric carcinoma invasion and metastasis.