bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of allele-specific methylation through a generalized heterogeneous epigenome model
Authors: Peng Qian , Ecker Joseph R. 
Published: June 2012

AbstractMotivations: High-throughput sequencing has made it possible to sequence DNA methylation of a whole genome at the single-base resolution. A sample, however, may contain a number of distinct methylation patterns. For instance, cells of different types and in different developmental stages may have different methylation patterns. Alleles may be differentially methylated, which may partially explain that the large portions of epigenomes from single cell types are partially methylated, and may have major effects on transcriptional output. Approaches relying on DNA sequence polymorphism to identify individual patterns from a mixture of heterogeneous epigenomes are insufficient as methylcytosines occur at a much higher density than SNPs.Results: We have developed a mixture model-based approach for resolving distinct epigenomes from a heterogeneous sample. In particular, the model is applied to the detection of allele-specific methylation (ASM). The methods are tested on a synthetic methylome and applied to an Arabidopsis single root cell methylome.Contact: qpeng@cs.ucsd.edu
Integration of environmental and fishery management in Europe
Authors: Jennings Simon , Le Quesne Will J. F. 
Published: June 2012

Abstract
Jennings, S., and Le Quesne, W. J. F. 2012. Integration of environmental and fishery management in Europe. – ICES Journal of Marine Science, 69: . Policy drivers for integrating environmental and fishery management in Europe have never been so strong. Scientists calling for better integration now have the opportunity to help deliver it. The main challenge is providing relevant evidence on short time-scales using existing knowledge. Policies, scientists, and society largely agree that management targets should be linked to achieving sustainability, but research often fails to show when fishing impacts ‘matter’ in relation to sustainability criteria. If targets for ecosystem functions or processes are to complement more tractable targets for species and habitats, scientists will need to show why impacts ‘matter’ and when they become unsustainable. For now, and to meet ambitious and pressing policy timetables, priority should be given to developing credible targets for impacts with a high risk of compromising sustainability, rather than dissipating research and advisory effort to achieve broader coverage of state, function, and process. Impacts on sensitive species and habitats often compromise sustainability; thus, setting targets for them is a priority. Meeting these targets will often require management measures that are expected to diminish risks of other unsustainable impacts. Fast and significant progress towards integration could be achieved by incorporating measures to meet environmental targets for sensitive species and habitats into fishery management plans.
A Medicago truncatula Tobacco Retrotransposon Insertion Mutant Collection with Defects in Nodule Development and Symbiotic Nitrogen Fixation
Authors: Pislariu Catalina I. , D. Murray Jeremy , Wen JiangQi , Cosson Viviane , Muni RajaSekhara Reddy Duvvuru , Wang Mingyi , A. Benedito Vagner , Andriankaja Andry , Cheng Xiaofei , Jerez Ivone Torres , Mondy Samuel , Zhang Shulan , Taylor Mark E. , Tadege Million , Ratet Pascal , Mysore Kirankumar S. , Chen Rujin , Udvardi Michael K. 
Published: June 2012

Abstract
A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod−), 51 mutants with totally ineffective nodules (Nod+ Fix−), 17 mutants with partially ineffective nodules (Nod+ Fix+/−), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/− Fix−), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/− Fix+), and 11 supernodulating mutants (Nod++Fix+/−). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN’T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod− lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.
Sea‐level and ocean‐current control on carbonate‐platform growth, Maldives, Indian Ocean
Authors: Betzler Christian , Fürstenau Jörn , Lüdmann Thomas , Hübscher Christian , Lindhorst Sebastian , Paul Andreas , Reijmer John J. G. , Droxler André W. 
Published: June 2012

AbstractMultichannel high‐resolution seismic and multibeam data were acquired from the Maldives‐isolated carbonate platform in the Indian Ocean for a detailed characterization of the Neogene bank architecture of this edifice. The goal of the research is to decipher the controlling factors of platform evolution, with a special emphasis on sea‐level changes and changes of the oceanic currents. The stacking pattern of Lower to Middle Miocene depositional sequences, with an evolution of a ramp geometry to a flat‐topped platform, reflects variations of accommodation, which here are proposed to be primarily governed by fluctuations of relative sea level. Easterly currents during this stage of bank growth controlled an asymmetric east‐directed progradation of the bank edge. During the late middle Miocene, this system was replaced by a twofold configuration of bank development. Bank growth continued synchronously with partial bank demise and associated sediment‐drift deposition. This turnover is attributed to the onset and/or intensification of the Indian monsoon and related upwelling and occurrence of currents, locally changing environmental conditions and impinging upon the carbonate system. Mega spill over lobes, shaped by reversing currents, formed as large‐scale prograding complexes, which have previously been interpreted as deposits formed during a forced regression. On a regional scale, a complex carbonate‐platform growth can occur, with a coexistence of bank‐margin progradation and aggradation, as well as partial drowning. It is further shown that a downward shift of clinoforms and offlapping geometries in carbonate platforms are not necessarily indicative for a sea‐level driven forced regression. Findings are expected to be applicable to other examples of Cenozoic platforms in the Indo‐Pacific region.
Assessment of environmental factors in disabled children 2–12 years: development and reliability of the Craig Hospital Inventory of Environmental Factors (CHIEF) for Children–Parent Version
Authors: McCauley D. , Gorter J. W. , Russell D. J. , Rosenbaum P. , Law M. , Kertoy M. 
Published: June 2012

AbstractBackground  Children with disabilities and their families experience environmental barriers in the school and community environments. There is a need to understand and appropriately measure environmental factors that influence activity and participation for disabled children. The purpose of this paper is to describe the adaptation process of the Craig Hospital Inventory of Environmental Factors (CHIEF) to make it suitable as a parent proxy measure for disabled children aged 2–12 years.Methods  The adaptation process consisted of four steps using data from previous research conducted at CanChild: (i) analysis of item–total correlations from all items on the CHIEF; (ii) frequency of endorsement; (iii) determination of the representativeness of the questions; and (iv) correlations on selected items. Once the items were selected, a test–retest reliability study was conducted.Results  The internal consistencies (α) for the time 1 and time 2 administrations were 0.76 and 0.78, respectively. Test–retest reliability of the questionnaire was ICC = 0.73 for the total product score.Conclusion  The 10‐item CHIEF for Children–Parent Version is an acceptable, easy‐to‐complete and reliable measure of perceived environmental barriers for disabled children 2–12 years of age.
Spanish version of the Sleep Self‐Report (SSR): factorial structure and psychometric properties
Authors: Orgilés M. , Owens J. , Espada J. P. , Piqueras J. A. , Carballo J. L. 
Published: June 2012

AbstractBackground  The Sleep Self‐Report (SSR) is a questionnaire initially created for use with a sample from the USA to assess sleep patterns and problems in school‐aged children. The objective of this study was to validate the SSR among a Spanish sample.Methods  Participants were 1228 Spanish children from 8 to 12 years of age who completed the questionnaires at school anonymously.Results  Internal consistency was good (ω= 0.85). Convergent validity with anxiety (r= 0.54) and perceived welfare (r=−0.53) measures, and divergent validity with a measure of academic performance and positive influence of peers (r=−0.22) were acceptable. Exploratory analysis suggested a factorial structure composed by four subscales: sleep quality, sleep anxiety, bedtime refusal and sleep routines. Confirmatory analysis indicated a good fit for the model (RMSEA = 0.04; GFI = 0.95; AGFI = 0.93; χ2/gl = 2.48).Conclusions  The SSR has demonstrated to have good psychometric properties in the Spanish‐speaking sample of children. The factorial structure supported by exploratory and confirmatory analysis examines the most relevant areas of sleep in children. The satisfactory psychometric properties support the use of the Spanish version of the SSR by researchers and clinicians.
A four‐part ecological model of community‐focused therapeutic recreation and life skills services for children and youth with disabilities
Authors: King G. , Curran C. J. , McPherson A. 
Published: June 2012

AbstractAim This article presents a four‐part model of community‐focused therapeutic recreation and life skills services for children's rehabilitation centres.Method and Results The model is based on 15 years of clinical and management practice in a Canadian context combined with evidence from the literature on community‐focused service delivery. The model incorporates an ecological approach and principles from models of therapeutic recreation, community capacity building, and health promotion, as well as client/family‐centred care. The four pillars of the model reflect a set of integrated services and principles designed to support the participation of children and youth with disabilities in community activities. The pillars involve providing community outreach services, providing community development services, sharing physical and educational resources with community partners, and promoting the organization as a community facility that provides adapted physical space and specialized instruction. The lessons learned in implementing the model are discussed, including the importance of ensuring the sustainability of community recreation programmes.Conclusions The model will be of use to managers and service organizations seeking to develop an integrated programme of community‐focused therapeutic recreation and life skills services based on a collaborative capacity‐building approach.
Do Chinese parents with HIV tell their children the truth? A qualitative preliminary study of parental HIV disclosure in China
Authors: Zhou Y. , Zhang L. , Li X. , Kaljee L. 
Published: June 2012

AbstractBackground  With the extended lifespan of people living with human immunodeficiency virus (HIV) due to the advent of antiretroviral therapy, the disclosure of HIV serostatus to their uninfected children is becoming more critical. However, limited data are available regarding parental HIV disclosure to children in China. We explore patterns of parental HIV disclosure and the reasons for disclosure or non‐disclosure to children.Methods  A preliminary study was conducted using open‐ended questions in Guangxi, China in 2011 with 39 parents living with HIV.Results  A majority of participants (77%) had not disclosed their HIV serostatus to their children. Participants who voluntarily disclosed tended to be older and were more likely to disclose to their adult children. Among parents who disclosed, reasons included a need for emotional and financial support, as well as feelings of obligation to their children. Among non‐disclosing parents, primary reasons included concerns that children were too young to understand, fear of being stigmatized, and fear of increased psychological burden to children.Conclusions  Few parents with HIV disclosed their HIV status to their children. These data indicate the need for future research to explore disclosure issues in relation to children's age and the implementation of developmentally appropriate interventions and support systems for parents and children affected by HIV in China.
Predictors of psychological adjustment, experienced parenting burden and chronic sorrow symptoms in parents of children with cerebral palsy
Authors: Whittingham K. , Wee D. , Sanders M. R. , Boyd R. 
Published: June 2012

AbstractAim  To investigate the role of child behaviour, parental coping and experiential avoidance in predicting the psychological outcomes of: (i) psychological symptoms; (ii) chronic sorrow symptoms; and (iii) experienced parenting burden in parents of children with cerebral palsy (CP).Method  This study is a cross‐sectional, correlational study. Ninety‐four parents of children (aged 2–12 years) with CP (various levels of motor functioning GMFCS I–V) participated.Results  Together, the three predictors of child behaviour, parental coping and experiential avoidance explained 36.8% of the variance in psychological symptoms with child behavioural problems and experiential avoidance as significant unique predictors. In addition, 15.8% of the variance in chronic sorrow symptoms was explained by the three predictors with experiential avoidance alone as a significant unique predictor. Lastly, the predictors together explained 24.3% of the variance in experienced parenting burden with child behavioural problems and experiential avoidance as significant unique predictors.Conclusions  This study demonstrates a relationship between child behavioural problems and parental psychological symptoms and experienced parenting burden as well as a relationship between experiential avoidance and parental psychological symptoms, experienced parenting burden and chronic sorrow symptoms.
The role of endothelial cell adhesion molecules P‐selectin, E‐selectin and intercellular adhesion molecule‐1 in leucocyte recruitment induced by exogenous methylglyoxal
Authors: Su Yang , Lei Xi , Wu Lingyun , Liu Lixin 
Published: June 2012

SummaryMethylglyoxal (MG) is a reactive dicarbonyl metabolite formed during glucose, protein and fatty acid metabolism. In hyperglycaemic conditions, increased MG level has been linked to the development of diabetes and its vascular complications at the macrovascular and microvascular levels where inflammation plays a role. To study the mechanism of MG‐induced inflammation in vivo, we applied MG locally to healthy mice and used intravital microscopy to investigate the role of endothelial cell adhesion molecules in MG‐induced leucocyte recruitment in cremasteric microvasculature. Administration of MG (25 and 50 mg/kg) to the tissue dose‐dependently induced leucocyte recruitment at 4·0–5·5 hr, with 84–92% recruited cells being neutrophils. Such MG treatment up‐regulated the expression of endothelial cell adhesion molecules P‐selectin, E‐selectin, intercellular adhesion molecule‐1, but not vascular cell adhesion molecule‐1. Activation of the nuclear factor‐κB signalling pathway contributed to MG‐induced up‐regulation of these adhesion molecules and leucocyte recruitment. The role of the up‐regulated endothelial cell adhesion molecules in MG‐induced leucocyte recruitment was determined by applying specific functional blocking antibodies to MG‐treated animals and observing changes in leucocyte recruitment parameters. Our data demonstrate that the up‐regulation of P‐selectin, E‐selectin and intercellular adhesion molecule‐1 contributes to the increased leucocyte rolling flux, reduced leucocyte rolling velocity, and increased leucocyte adhesion, respectively. Our results reveal the role of endothelial cell adhesion molecules in MG‐induced leucocyte recruitment in microvasculature, an inflammatory condition related to diabetic vascular complications.
Phylogeography and molecular phylogeny of Macaronesian island Tarphius (Coleoptera: Zopheridae): why are there so few species in the Azores?
Authors: Amorim Isabel R. , Emerson Brent C. , Borges Paulo A. V. , Wayne Robert K. 
Published: June 2012

AbstractAim  We used a phylogenetic framework to examine island colonization and predictions pertaining to differentiation within Macaronesian Tarphius (Insecta, Coleoptera, Zopheridae), and explain the paucity of endemics in the Azores compared with other Macaronesian archipelagos. Specifically, we test whether low diversity in the Azores could be due to recent colonization (phylogenetic lineage youth), cryptic speciation (distinct phylogenetic entities within species) or the young geological age of the archipelago.Location  Macaronesian archipelagos (Azores, Madeira and the Canary Islands), northern Portugal and Morocco.Methods  Phylogenetic analyses of mitochondrial and nuclear genes of Tarphius beetles of the Azores, other Macaronesian islands and neighbouring continental areas were used to investigate the origin of island biodiversity and to compare patterns of colonization and differentiation. A comparative nucleotide substitution rate test was used to select the appropriate substitution rate to infer clade divergence times.Results  Madeiran and Canarian Tarphius species were found to be more closely related to each other, while Azorean taxa grouped separately. Azorean taxa showed concordance between species and phylogenetic clades, except for species that occur on multiple islands, which segregated by island of origin. Divergence time estimates revealed that Azorean Tarphius are an old group and that the most recent intra‐island speciation event on Santa Maria, the oldest island, occurred between 3.7 and 6.1 Ma.Main conclusions  Our phylogenetic approach provides new evidence to understand the impoverishment of Azorean endemics: (1) Tarphius have had a long evolutionary history within the Azores, which does not support the hypothesis of fewer radiation events due to recent colonization; (2) the current taxonomy of Azorean Tarphius does not reflect common ancestry and cryptic speciation is responsible for the underestimation of endemics; (3) intra‐island differentiation in the Azores was found only in the oldest island, supporting the idea that young geological age of the archipelago limits the number of endemics; and (4) the lack of evidence for recent intra‐island diversification in Santa Maria could also explain the paucity of Azorean endemics. Phylogenetic reconstructions of other species‐rich taxa that occur on multiple Macaronesian archipelagos will reveal whether our conclusions are taxon specific, or of a more general nature.
Language development in school‐age girls with fragile X syndrome
Authors: Sterling A. , Abbeduto L. 
Published: June 2012

AbstractBackground  Girls with fragile X syndrome (FXS) have a wide range of cognitive and language abilities. The range of language outcomes experienced by girls with FXS, however, has been relatively unexplored. The purpose of this exploratory study was to examine receptive and expressive language, with a focus on vocabulary and syntax, in a group of school‐age girls with FXS.Method  Twenty‐one girls with FXS aged 7–15 years participated in the study. The girls completed a receptive vocabulary test, non‐verbal IQ test and an expressive language sample.Results  The mean IQ for this group of girls was at the cut‐off for intellectual disability. Vocabulary was an area of strength relative to non‐verbal cognition. Age and non‐verbal IQ were significant predictors of vocabulary performance.Conclusions  The data suggest that a substantial portion of the sample would qualify for speech and language services. This study highlights the need for continued research in the area of language and cognitive development in girls with the full mutation of fragile X.
What are the potential outcomes of integrating emotionally competent behaviours into the care of psychiatric patients?
Authors: DOAS M. D. 
Published: June 2012

Accessible summary
Psychiatric nurses regularly encounter stressful clinical situations.
Today's challenging behavioural/psychiatric healthcare environments may impede a nurse's ability to demonstrate emotionally competent behaviours.
Emotional competence refers to one's ability to effectively express or release inner feelings. It also implies mutual respect for others and the ability to effectively communicate and participate in productive interpersonal interactions.
Emotionally competent nurses effectively deal with their emotions in stressful situations without suppressing others or their emotions.
AbstractThis descriptive study explored the concept of emotional competence in inpatient psychiatric nurse's daily interactions. Psychiatric registered nurses were asked to identify interactions of emotional competence they experienced on the nursing unit. Content analysis revealed deficits in self‐awareness, mood management and managing relationships.
Regional differences in cortical electroencephalogram (EEG) slow wave activity and interhemispheric EEG asymmetry in the fur seal
Authors: LYAMIN OLEG I. , PAVLOVA IVETTA F. , KOSENKO PETER O. , MUKHAMETOV LEV M. , SIEGEL JEROME M. 
Published: June 2012

SummarySlow wave sleep (SWS) in the northern fur seal (Callorhinus ursinus) is characterized by a highly expressed interhemispheric electroencephalogram (EEG) asymmetry, called ‘unihemispheric’ or ‘asymmetrical’ SWS. The aim of this study was to examine the regional differences in slow wave activity (SWA; power in the range of 1.2–4.0 Hz) within one hemisphere and differences in the degree of interhemispheric EEG asymmetry within this species. Three seals were implanted with 10 EEG electrodes, positioned bilaterally (five in each hemisphere) over the frontal, occipital and parietal cortex. The expression of interhemispheric SWA asymmetry between symmetrical monopolar recordings was estimated based on the asymmetry index [AI = (L−R)/(L+R), where L and R are the power in the left and right hemispheres, respectively]. Our findings indicate an anterior–posterior gradient in SWA during asymmetrical SWS in fur seals, which is opposite to that described for other mammals, including humans, with a larger SWA recorded in the parietal and occipital cortex. Interhemispheric EEG asymmetry in fur seals was recorded across the entire dorsal cerebral cortex, including sensory (visual and somatosensory), motor and associative (parietal or suprasylvian) cortical areas. The expression of asymmetry was greatest in occipital–lateral and parietal derivations and smallest in frontal–medial derivations. Regardless of regional differences in SWA, the majority (90%) of SWS episodes with interhemispheric EEG asymmetry meet the criteria for ‘unihemispheric SWS’ (one hemisphere is asleep while the other is awake). The remaining episodes can be described as episodes of bilateral SWS with a local activation in one cerebral hemisphere.