bluuebunny/crossref_metadata_2025 huggingface dataset:
Hadoop-BAM: directly manipulating next generation sequencing data in the cloud
Authors: Niemenmaa Matti , Kallio Aleksi , Schumacher André , Klemelä Petri , Korpelainen Eija , Heljanko Keijo
Published: February 2012

Summary: Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions that can directly operate on BAM records. It builds on top of the Picard SAM JDK, so tools that rely on the Picard API are expected to be easily convertible to support large-scale distributed processing. In this article we demonstrate the use of Hadoop-BAM by building a coverage summarizing tool for the Chipster genome browser. Our results show that Hadoop offers good scalability, and one should avoid moving data in and out of Hadoop between analysis steps.

Availability: Available under the open-source MIT license at http://sourceforge.net/projects/hadoop-bam/

Contact:  matti.niemenmaa@aalto.fi

Supplementary information:  Supplementary material is available at Bioinformatics online.
Evaluating the Drosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts
Authors: He Feng , Ren Jie , Wang Wei , Ma Jun
Published: February 2012

Motivation: We describe a statistical model to dissect the noise in transcriptional bursts in a developmental system.

Results: We assume that, at any given moment of time, each copy of a native gene inside a cell can exist in either a bursting (active) or non-bursting (inactive) state. The experimentally measured total noise in the transcriptional states of a gene in a population of cells can be mathematically dissected into two contributing components: internal and external. While internal noise quantifies the stochastic nature of transcriptional bursts, external noise is caused by cell-to-cell differences including fluctuations in activator concentration. We use our developed methods to analyze the Drosophila Bicoid (Bcd) morphogen gradient system. For its target gene hunchback (hb), the noise properties can be recapitulated by a simplified gene regulatory model in which Bcd acts as the only input, suggesting that the external noise in hb transcription is primarily derived from fluctuations in the Bcd activator input. However, such a simplified gene regulatory model is insufficient to predict the noise properties of another Bcd target gene, orthodenticle (otd), suggesting that otd transcription is sensitive to additional external fluctuations beyond those in Bcd. Our results show that analysis of the relationship between input and output noise can reveal important insights into how a morphogen gradient system works. Our study also advances the knowledge about transcription at a fundamental level.

Contact:  jun.ma@cchmc.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Parental Knowledge of Fecal Incontinence in Children
Authors: van Tilburg Miranda A.L. , Squires Megan , Blois‐Martin Nanette , Williams Cathy , Benninga Marc A. , Peeters Babette , Ulshen Martin
Published: February 2012

Objectives:

Fecal incontinence (FI) is a common and stressful symptom of constipation in children. Recurrent FI causes psychological and physiological changes, complicating treatment as symptom duration progresses; however, parental misconceptions about the causes of FI may delay seeking medical care. The aim of the present study was to assess parental knowledge about FI and determine how this relates to the care and treatment of FI.

Methods:

A questionnaire was developed from qualitative interviews and clinician input. The questionnaire was administered to 251 parents and tested for reliability and validity. Subscales were compared between parents who did and did not consult a clinician. In addition, 30 parents completed the questionnaire before and after consultation with a pediatric gastroenterologist and after 2 months of treatment.

Results:

Two subscales were identified with good psychometric properties: “Blame and Punish” and “Worry and Help.” Families who consulted a physician for their child's FI acknowledged the role of constipation and scored higher on Worry and Help (mean 36.4 vs mean 46.9; P < 0.0001). Trends were found for Blame and Punish to decrease after consultation with a pediatric gastroenterologist (mean 1.7 vs 1.5; P = 0.08) and after 2 months of treatment (mean 1.5; P = 0.08).

Conclusions:

Parental knowledge about FI changes with physician consultation. These findings can help in developing educational materials for parents to encourage early diagnosis and treatment and prevent chronic problems that are difficult to manage.
Histamine reduces susceptibility to natural killer cells via down‐regulation of NKG2D ligands on human monocytic leukaemia THP‐1 cells
Authors: Nagai Yasuhiro , Tanaka Yukinori , Kuroishi Toshinobu , Sato Ryutaro , Endo Yasuo , Sugawara Shunji
Published: February 2012

Natural killer (NK) group 2D (NKG2D) is a key activating receptor expressed on NK cells, whose interaction with ligands on target cells plays an important role in tumorigenesis. However, the effect of histamine on NKG2D ligands on tumour cells is unclear. Here we showed that human monocytic leukaemia THP‐1 cells constitutively express MHC class I‐related chain A (MICA) and UL16‐binding protein 1 on their surface, and incubation with histamine reduced the expression in a dose‐dependent and time‐dependent manner as assessed by flow cytometry. Interferon‐γ augmented the surface expression of the NKG2D ligands, and this augmentation was significantly attenuated by histamine. The histamine H1 receptor (H1R) agonist 2‐pyridylethylamine and H2R agonist dimaprit down‐regulated the expression of NKG2D ligands, and activation of H1R and H2R signalling by A23187 and forskolin, respectively, had the same effect, indicating that the histamine‐induced down‐regulation of NKG2D ligands is mediated by H1R and H2R. Quantitative reverse transcription‐PCR showed that mRNA levels of the NKG2D ligands and relevant microRNAs were not significantly changed by histamine. Histamine down‐regulated the surface expression of endoplasmic reticulum protein 5, and inhibition of matrix metalloproteinases did not impair this down‐regulation, indicating that proteolytic shedding was not involved. Instead, pharmacological inhibition of protein transport and proteasome abrogated it, and histamine enhanced ubiquitination of MICA. Furthermore, histamine treatment significantly reduced susceptibility to NK cell‐mediated cytotoxicity. These results suggest that histamine down‐regulates NKG2D ligands through the activation of an H1R‐ and H2R‐mediated ubiquitin–proteasome pathway and consequently reduces susceptibility to NK cells.
S100A9 a new marker for monocytic human myeloid‐derived suppressor cells
Authors: Zhao Fei , Hoechst Bastian , Duffy Austin , Gamrekelashvili Jaba , Fioravanti Suzanne , Manns Michael P. , Greten Tim F. , Korangy Firouzeh
Published: February 2012

Myeloid‐derived suppressor cells (MDSC) are a heterogeneous population of cells that negatively regulate the immune response during tumour progression, inflammation and infection. Only limited data are available on human MDSC because of the lack of specific markers. We have identified members of the S100 protein family – S100A8, S100A9 and S100A12 – specifically expressed in CD14+ HLA‐DR−/low MDSC. S100A9 staining in combination with anti‐CD14 could be used to identify MDSC in whole blood from patients with colon cancer. An increase in the population of CD14+ S100A9high MDSC was observed in the peripheral blood from colon cancer patients in comparison with healthy controls. Finally, nitric oxide synthase expression, a hallmark of MDSC, was induced in CD14+ S100A9high upon lipopolysaccharide/interferon‐γ stimulation. We propose S100 proteins as useful markers for the analysis and further characterization of human MDSC.
A national survey of the use of physical restraint in long‐term care hospitals in Japan
Authors: Chiba Yumi , Yamamoto‐Mitani Noriko , Kawasaki Maki
Published: February 2012

Aims and objectives.  To investigate the prevalence of physical restraints in the long‐term care hospitals in Japan and to examine the factors of physical restraint use, including the specific skills/techniques that the staff use to minimise the restraints.

Background.  Despite the national efforts to nullify physical restraint, it is still prevalent in long‐term care facilities in and out of Japan. More detailed information regarding what affects physical restraint is needed.

Design.  Cross‐sectional mail survey.

Method.  A questionnaire was sent to a nursing ward manager of the random sample of long‐term care facilities in Japan.

Results.  The average rate of physical restraint was 25·5%. Altogether, 81·0% of the restrained clients were under restraint for more than one month. The most prevalent method of restraint was bilateral bedrails, followed by the use of coveralls and gloves. Factors of restraint were different depending on the type of restraint, suggesting specific approaches are needed for specific type of restraint.

Conclusions.  Physical restraint is still prevalent in Japanese long‐term care hospitals, and nurses need to develop effective intervention approach to redesigning practice related to physical restraints. Specialised intervention approach seems needed depending on the types of restraint.

Relevance to clinical practice.  Specific approach should be developed to minimise the physical restraint in long‐term care hospitals in Japan.
Total and differential leucocyte counts in relation to incidence of stroke subtypes and mortality: a prospective cohort study
Authors: Zia E. , Melander O. , Björkbacka H. , Hedblad B. , Engström G.
Published: February 2012

Abstract.  Zia E, Melander O, Björkbacka H, Hedblad B, Engström G (Lund University, Malmö; Institute of Clinical Sciences, Lund University, Malmö; Skåne University Hospital, Malmö; and Astra Zeneca R&D, Malmö, Sweden). Total and differential leucocyte counts in relation to incidence of stroke subtypes and mortality: a prospective cohort study. J Intern Med 2012; 272: 298–304.

Objectives.  Elevated levels of total leucocyte as well as leucocyte subtypes have been associated with increased risk of atherosclerotic disease. Atherosclerosis is an important cause of cerebral infarction, whereas its significance in intracerebral haemorrhage (ICH) is less clear. A small number of prospective studies have revealed the relationship between leucocyte counts and incident stroke, in particular incidence of stroke subtypes. We evaluated the associations between total leucocyte count (TLC) as well as leucocyte subtypes and the incidence of and mortality caused by different stroke subtypes.

Design and subjects.  Of 28 449 participants from the Malmö Diet and Cancer Study, 26 927 stroke‐free subjects (mean age at screening, 58 ± 8 years) were included in a prospective cohort study. The screening period was between 1991 and 1996. Incidence of stroke, 1‐year mortality and 1‐month case‐fatality rate (CFR) were assessed by linkage to local and national registers. Cox regression analysis was used to assess stroke risk and 1‐year mortality, and 1‐month CFR was assessed by logistic regression analysis.

Results.  During a follow‐up period of 13.6 ± 3.3 years, 1515 participants had a first‐ever stroke (cerebral infarction, n = 1314; ICH, n = 201). After adjustments for other risk factors, TLC and neutrophil count were significantly associated with increased incidence of cerebral infarction (hazards ratio (HR), 1.4; 95% confidence interval (CI), 1.2–1.7 and 1.3; 95% CI, 1.1–1.5, respectively). There was an inverse association between elevated TLC and incident ICH (HR, 0.7; 95% CI, 0.4–0.99). No associations were found between leucocyte counts and mortality for either stroke subtype.

Conclusion.  The results suggest that the relationships with inflammation for ischaemic stroke and ICH are different.
Duodenal lipid‐induced symptom generation in gastroesophageal reflux disease: role of apolipoprotein A‐IV and cholecystokinin
Authors: van Boxel O. S. , ter Linde J. J. M. , Oors J. , Otto B. , Feinle‐Bisset C. , Smout A. J. P. M. , Siersema P. D.
Published: February 2012

Background  Duodenal lipid intensifies the perception of esophageal acid perfusion. Recently, we showed that genes implicated in lipid absorption were upregulated in the duodenum of fasting gastro‐esophageal reflux disease (GERD) patients. This suggests that chylomicron production and secretion may be enhanced and, consequently, the release of apolipoprotein A‐IV (apoA‐IV), a chylomicron‐derived signaling protein. ApoA‐IV may stimulate release of cholecystokinin (CCK), an activator of vagal afferents. This study evaluated putative involvement of abnormal apoA‐IV and CCK responses to lipid in GERD.

Methods  Ten GERD patients and 10 healthy volunteers (HV) underwent duodenal perfusion with Intralipid 20%, 2 kcal min−1, for 60 min. Symptoms were scored, blood samples collected every 15 min during lipid perfusion and 15 min after discontinuation when duodenal biopsies were taken. Plasma and mucosal concentrations of apoA‐IV and CCK and transcript levels of 21 genes implicated in lipid absorption, differentially expressed under fasting conditions, were quantified.

Key Results  Heartburn (P = 0.003), abdominal discomfort (P = 0.037) and nausea (P = 0.008) only increased significantly during lipid infusion in GERD patients. Following lipid infusion mean mucosal apoA‐IV concentration was lower in GERD patients compared with HV (P = 0.023), whereas plasma concentration tended to be elevated (P = 0.068). Mean mucosal CCK concentration was also lower in GERD patients (P = 0.009). Two genes, HIBADH and JTB, were upregulated in GERD patients (P = 0.008 and P = 0.038, respectively).

Conclusions & Inferences  Our results suggest excessive duodenal lipid‐induced release of apoA‐IV and CCK in GERD. We postulate that the resulting heightened activation of duodenal vagal afferents may underlie central sensitization, thereby increasing the perception of reflux events.
Evaluation of the antifungal susceptibility of Malassezia pachydermatis to clotrimazole, miconazole and thiabendazole using a modified CLSI M27‐A3 microdilution method
Authors: Peano Andrea , Beccati Massimo , Chiavassa Elisa , Pasquetti Mario
Published: February 2012

Background –  In this study, we evaluated the antifungal susceptibility of Malassezia pachydermatis to clotrimazole (CTZ), miconazole (MCZ), and thiabendazole (TBD), azole derivatives employed in aural formulations labeled for treatment of canine otitis.

Methods –  The procedure for in vitro testing was based on the indications of the Clinical and Laboratory Standards Institute (CLSI) M27‐A3 microdilution method. A lipid‐enriched medium was employed to enhance the yeast growth (Christensen’s urea broth, with 0.1% Tween 80 and 0.5% Tween 40 as the lipid sources), while the inoculums size corresponded to approximately 1–5 × 105 yeast cells/mL. Microplates were incubated at 37°C and read 48 h after inoculation. Azole MICs inhibiting fungal growth were the lowest drug concentrations that showed an optical density of ≤50% of the (drug‐free) growth control, as assessed by spectrophotometer (630 nm filter).

Results –  All isolates were inhibited by the three azoles, with different minimum inhibitory concentration (MIC) values. Most isolates were inhibited by drug concentrations of 2–8 (CTZ), 1–4 (MCZ), or 16–32 (TBD) μg/mL. These results are partially in agreement with the findings of previous studies, in which substantially higher/lower MICs were occasionally reported. This is likely because of the different methodologies employed. Such discrepancies may not apply to clinical situations, where the compounds are applied topically.

Conclusion and clinical importance –  The concept that clinical failure is linked to increased MICs is debatable, because significantly higher concentrations (in most cases at least 1,000 × the MIC) of the antifungals that were included in our study are routinely used in formulated products.
Cough and dyspnoea may discriminate allergic and infectious respiratory phenotypes in infancy
Authors: Rancière Fanny , Clarisse Bénédicte , Nikasinovic Lydia , Just Jocelyne , Momas Isabelle
Published: February 2012

To cite this article: Rancière F, Clarisse B, Nikasinovic L, Just J, Momas I. Cough and dyspnoea may discriminate allergic and infectious respiratory phenotypes in infancy. Pediatr Allergy Immunol 2012: 23: 367–375.

Asthma symptoms are non‐specific during infancy, making the identification of different subgroups among preschool children with early respiratory manifestations an important challenge. We previously used a clustering approach to identify bronchial obstructive phenotypes in 1‐yr‐old infants from the Pollution and Asthma Risk: an Infant Study (PARIS) birth cohort. In the present study, we examined whether these phenotypes were stable at 3 yr and studied their comorbidity and risk factors. Partitioning around medoids (PAM) method was applied at 1 and 3 yr of age to cluster children according to wheezing, dry night cough, dyspnoea with sleep disturbance and breathlessness. The resulting groups were used to derive phenotypes in 2084 children during their first 3 yr of life. Analysis of associated comorbidity and risk factors was conducted using multinomial logistic regression. PAM groups were similarly defined at both ages so that two respiratory phenotypes were identified between birth and 3 yr: cough phenotype (CP) and dyspnoea phenotype (DP) including 14.1% and 30.7% of children, respectively. CP infants experienced more often allergic features than DP, dominated by respiratory infections. Parental history of allergy, potential allergen exposure and psychosocial factors were associated with CP. Day care centre attendance was more frequent in DP as well as exposure to domestic chemical pollution, suggesting a greater vulnerability to pathogens. Finally, dry night cough and dyspnoea disturbing the sleep appear to be markers of two respiratory profiles potentially allergic and infectious before 3 yr old.
Direct experimental evidence that early‐life farm environment influences regulation of immune responses
Authors: Lewis Marie C. , Inman Charlotte F. , Patel Dilip , Schmidt Bettina , Mulder Imke , Miller Bevis , Gill Bhupinder P. , Pluske John , Kelly Denise , Stokes Christopher R. , Bailey Michael
Published: February 2012

To cite this article: Lewis MC, Inman CF, Patel D, Schmidt B, Mulder I, Miller B, Gill BP, Pluske J, Kelly D, Stokes CR, Bailey M. Direct experimental evidence that early‐life farm environment influences regulation of immune responses. Pediatr Allergy Immunol 2012: 23: 265–269.

Background:  In mammals, early‐life environmental variations appear to affect microbial colonization and therefore competent immune development, and exposure to farm environments in infants has been inversely correlated with allergy development. Modelling these effects using manipulation of neonatal rodents is difficult due to their dependency on the mother, but the relatively independent piglet is increasingly identified as a valuable translational model for humans. This study was designed to correlate immune regulation in piglets with early‐life environment.

Methods:  Piglets were nursed by their mother on a commercial farm, while isolator‐reared siblings were formula fed. Fluorescence immunohistology was used to quantify T‐reg and effector T‐cell populations in the intestinal lamina propria and the systemic response to food proteins was quantified by capture ELISA.

Results:  There was more CD4+ and CD4+CD25+ effector T‐cell staining in the intestinal mucosa of the isolator‐reared piglets compared with their farm‐reared counterparts. In contrast, these isolator‐reared piglets had a significantly reduced CD4+CD25+Foxp3+ regulatory T‐cell population compared to farm‐reared littermates, resulting in a significantly higher T‐reg‐to‐effector ratio in the farm animals. Consistent with these findings, isolator‐reared piglets had an increased serum IgG anti‐soya response to novel dietary soya protein relative to farm‐reared piglets.

Conclusion:  Here, we provide the first direct evidence, derived from intervention, that components of the early‐life environment present on farms profoundly affects both local development of regulatory components of the mucosal immune system and immune responses to food proteins at weaning. We propose that neonatal piglets provide a tractable model which allows maternal and treatment effects to be statistically separated.
Perspectives on immunomodulation early in life
Authors: Diesner Susanne C. , Förster‐Waldl Elisabeth , Olivera Ana , Pollak Arnold , Jensen‐Jarolim Erika , Untersmayr Eva
Published: February 2012

To cite this article: Diesner SC, Förster‐Waldl E, Olivera A, Pollak A, Jensen‐Jarolim E, Untersmayr E. Perspectives on immunomodulation early in life. Pediatr Allergy Immunol 2012: 23: 210–223.

The immune system early in life is characterized by immature activation and function of immune cells and a preponderance of Th2 cytokines. Together with other factors such as genetics and epigenetics, these immature immune responses might prone newborns susceptible to severe infections as well as allergic diseases. Immunomodulation therapy may have potential as therapeutic strategy against those disorders and might have implication in early‐life interventions in the future. In this review, we will focus on two immunomodulatory substance classes, Toll‐like receptor (TLR) ligands and sphingolipids, which are the focus of extensive research to date. Both TLRs and sphingolipid receptors have a very distinct distribution pattern and function on immune cells. Therefore, they can potentially modulate and balance immune responses, which might be in particular beneficial for the immaturity of the immune response early in life.
Differential response of radish plants to supplemental ultraviolet‐B radiation under varying NPK levels: chlorophyll fluorescence, gas exchange and antioxidants
Authors: Singh Suruchi , Kumari Rima , Agrawal Madhoolika , Agrawal Shashi Bhushan
Published: February 2012

Current and projected increases in ultraviolet‐B (UV‐B; 280–315 nm) radiation may alter crop growth and yield by modifying the physiological and biochemical functions. This study was conducted to assess the possibility of alleviating the negative effects of supplemental UV‐B (sUV‐B; 7.2 kJ m−2 day−1; 280–315 nm) on radish (Raphanus sativus var Pusa Himani) by modifying soil nitrogen (N), phosphorus (P) and potassium (K) levels. The N, P and K treatments were recommended dose of N, P and K, 1.5 times recommended dose of N, P and K, 1.5 times recommended dose of N and 1.5 times recommended dose of K. Plants showed variations in their response to UV‐B radiation under varying soil NPK levels. The minimum damaging effects of sUV‐B on photosynthesis rate and stomatal conductance coupled with minimum reduction in chlorophyll content were recorded for plants grown at recommended dose of NPK. Flavonoids increased under sUV‐B except in plants grown at 1.5 times recommended dose of N. Lipid peroxidation (LPO) also increased in response to sUV‐B at all NPK levels with maximum at 1.5 times recommended dose of K and minimum at recommended dose of NPK. This study revealed that sUV‐B radiation negatively affected the radish plants by reducing the photosynthetic efficiency and increasing LPO. The plants grown at 1.5 times recommended dose of NPK/N/K could not enhance antioxidative potential to the extent as recorded at recommended dose of NPK and hence showed more sensitivity to sUV‐B.
The phytohormone auxin is a component of the regulatory system that controls UV‐mediated accumulation of flavonoids and UV‐induced morphogenesis
Authors: Hectors Kathleen , van Oevelen Sandra , Guisez Yves , Prinsen Els , Jansen Marcel A. K.
Published: February 2012

In plants, ultraviolet (UV)‐B acclimation is a complex, dynamic process that plays an essential role in preventing UV‐B damage to targets such as DNA and the photosynthetic machinery. In this study we tested the hypothesis that the phytohormone auxin is a component of the regulatory system that controls both UV‐mediated accumulation of flavonoids and UV‐induced morphogenesis. We found that the leaf area of Arabidopsis thaliana Col‐0 plants raised under a low dose of UV radiation (0.56 kJ m−2 daily dose) was, on average, decreased by 23% relative to plants raised in the absence of UV‐B, and this was accompanied by a decrease (P = 0.063) in free auxin in young leaf tissues. Compared to Col‐0, both the auxin influx mutant axr4‐1 and the auxin biosynthesis mutant nit1‐3 displayed significantly stronger morphogenic responses, i.e. relative decreases in leaf area were greater for these two mutants. UV exposure also induced accumulation of flavonoids. In Col‐0, increases in the concentrations of specific kaempferol derivatives ranged from 2.1‐ to 19‐fold. Thus, UV induces complex changes in flavonoid–glycosylation patterns. Compared to Col‐0, three auxin mutants displayed significantly different flavonoid profiles. Thus, based on mutant analysis, it is concluded that the phytohormone auxin plays a role in UV acclimation by regulating flavonoid concentration, flavonoid–glycosylation pattern and by controlling UV‐induced morphogenic responses.
Influence of model specifications on the reliabilities of genomic prediction in a Swedish–Finnish red breed cattle population
Authors: Rius‐Vilarrasa E. , Brøndum R.F. , Strandén I. , Guldbrandtsen B. , Strandberg E. , Lund M.S. , Fikse W.F.
Published: February 2012

Using a combined multi‐breed reference population, this study explored the influence of model specification and the effect of including a polygenic effect on the reliability of genomic breeding values (DGV and GEBV). The combined reference population consisted of 2986 Swedish Red Breed (SRB) and Finnish Ayrshire (FAY) dairy cattle. Bayesian methodology (common prior and mixture models with different prior distribution settings for the marker effects) as well as a best linear unbiased prediction with a genomic relationship matrix [genomic best linear unbiased predictor (GBLUP)] was used in the prediction of DGV. Mixture models including a polygenic effect were used to predict GEBV. In total, five traits with low, high and medium heritability were analysed. For the models using a mixture prior distribution, reliabilities of DGV tended to decrease with an increasing proportion of markers with small effects. The influence of the inclusion of a polygenic effect on the reliability of DGV varied across traits and model specifications. Average correlation between DGV with the Mendelian sampling term, across traits, was highest (R2 = 0.25) for the GBLUP model and decreased with increasing proportion of markers with large effects. Reliabilities increased when DGV and parent average information were combined in an index. The GBLUP model with the largest gain across traits in the reliability of the index achieved the highest DGV mean reliability. However, the polygenic models showed to be less biased and more consistent in the estimation of DGV regardless of the model specifications compared with the mixture models without the polygenic effect.
Leaf breakdown in an Atlantic Rain Forest stream
Authors: GONÇALVES JR JOSÉ F. , REZENDE RENAN S. , MARTINS NARLIANE M. , GREGÓRIO RENER S.
Published: February 2012

The hypothesis of this study was that colonizers in decaying leaf litter prefer native species (Erythrina verna) to exotic ones (Eucalyptus camaldulensis and Protium heptaphyllum). Therefore, native species are expected to show higher breakdown rates, increased biomass, richness and density of invertebrate species, and increased biomass of decomposer fungi. Breakdown of leaf litter from these three species was assessed in an Atlantic Rain Forest stream. Four samples were collected during a period of 90 days and washed on a sieve to separate the invertebrates. Then, a series of leaf disks were cut to determine ash‐free dry mass and fungal biomass, and the remaining material was oven‐dried to determine the dry weight. Eucalyptus camaldulensis and E. verna showed higher breakdown rates than P. heptaphyllum, due to differences in leaf physical and chemical characteristics. The harder detritus (P. heptaphyllum) broke down more slowly than detritus with high concentrations of labile compounds (E. camaldulensis). The density of the invertebrates associated with detritus increased with time. There were no differences in density, taxonomic richness or biomass of invertebrates among the leaf types, which indicated that the invertebrates did not distinguish between exotic and native detritus. Fungal colonization varied among samples; E. camaldulensis showed the lowest ergosterol concentrations, mainly due to a high concentration of total phenolics. The detritus with the highest hardness value was colonized most slowly by fungi. These results showed that leaf breakdown in Atlantic Rain Forest streams could be affected either by changes in riparian vegetation, or by becoming more savanna‐like process due to climate change.
Speciation and dietary specialization in Drupa, a genus of predatory marine snails (Gastropoda: Muricidae)
Authors: Claremont Martine , Reid David G. , Williams Suzanne T.
Published: February 2012

Claremont, M., Reid, D.G. & Williams, S.T. (2012) Speciation and dietary specialization in Drupa, a genus of predatory marine snails (Gastropoda: Muricidae). —Zoologica Scripta, 41, 137–149.

We test the competing predictions of allopatric speciation and of ecological speciation by dietary specialization in Drupa, an Indo‐Pacific genus of carnivorous marine gastropods in the family Muricidae. We use a well‐resolved molecular phylogeny (reconstructed from one nuclear and two mitochondrial genes) to show the validity of the traditional species D. elegans, D. rubusidaeus, D. clathrata, D. morum and D. speciosa.‘Drupa ricinus’ is shown to consist of three species: D. ricinus s. s., D. albolabris and a new species, possibly endemic to Japan. ‘Purpura’aperta is transferred to Drupa. Despite potential widespread dispersal and a high degree of range overlap among sister species, range sizes between sister species are highly asymmetric, suggesting that speciation has been predominately peripatric. The exception is the sister pair D. ricinus s. s. and D. albolabris, which have symmetric range sizes and are sympatric over broad Indo‐Pacific ranges. Such symmetry and extensive sympatry are contrary to the predictions of the (peripatric) allopatric model of speciation. Nevertheless, contrary to the predictions of an ecological speciation model based upon dietary specialization, broad dietary range appears to be identical between the species. Small differences in microhabitat preferences (or hypothetical dietary specialization at a fine taxonomic scale) may have been significant in the speciation process or, if initial divergence was allopatric, in permitting subsequent sympatry. Broad dietary shifts appear to have accompanied more ancient divergences within the genus Drupa.
The Mind Behind the Message: Advancing Theory‐of‐Mind Scales for Typically Developing Children, and Those With Deafness, Autism, or Asperger Syndrome
Authors: Peterson Candida C. , Wellman Henry M. , Slaughter Virginia
Published: February 2012

Children aged 3–12 years (n = 184) with typical development, deafness, autism, or Asperger syndrome took a series of theory‐of‐mind (ToM) tasks to confirm and extend previous developmental scaling evidence. A new sarcasm task, in the format of H. M. Wellman and D. Liu’s (2004) 5‐step ToM Scale, added a statistically reliable 6th step to the scale for all diagnostic groups. A key previous finding, divergence in task sequencing for children with autism, was confirmed. Comparisons among diagnostic groups, controlling age, and language ability, showed that typical developers mastered the 6 ToM steps ahead of each of the 3 disabled groups, with implications for ToM theories. The final (sarcasm) task challenged even nondisabled 9‐year‐olds, demonstrating the new scale’s sensitivity to post‐preschool ToM growth.
A Polynomial Parametric Curve (PPC‐CURVE) for the Design of Horizontal Geometry of Highways
Authors: Bosurgi G. , D’Andrea A.
Published: February 2012

Abstract:  The use of transition curves in the road design is a solution to make the gradual evolution of curvature and, at the same time, to improve the comfort level of drivers and provide a good visual perception of the curve. Clothoid is the most widely used transition curve in road design so far, because it ensures the continuity of the curvature with the other geometric elements of the alignment.

However, several researches allow the use of polynomial functions as an alternative to the clothoid. Such use is permitted in accordance with the verification of allowable vehicle–road dynamics.

Polynomial solutions of transition curves can be a valuable alternative for the traditional solutions (first transition curve, circular arc, second transition curve).

A fifth‐degree polynomial parametric curve (PPC‐curve) for the design of highway alignment is proposed in this article. An analysis of the theoretical aspects to solve more complex geometrical problems recurring in practical highway geometric design is carried out. With regard to this problem, a shape parameter giving flexibility to the polynomial solution in relation to project needs has also been introduced.

To implement the procedure, an original computer program has been developed. Numerical applications have been performed for comparison with the traditional solutions.
Korean Children's Evaluation of Parental Restrictions Regarding Gender‐stereotypic Peer Activities
Authors: Park Yoonjung , Lee‐Kim Jennie , Killen Melanie , Park Kyoungja , Kim Jihyun
Published: February 2012

Korean children's evaluations of parental restrictions of children's activities based on gender stereotypic expectations were investigated. Third and sixth grade Korean (N = 128) children evaluated scenarios in which a boy or girl desired to play ballet or soccer. Participants used stereotypes to support children's desires to play gender‐consistent activities and adhered to parental authority for choice of gender‐consistent social activities. Yet, they also rejected parental decisions to treat sons and daughters differently based on the view that it would be unfair. Stereotypic expectations decreased with age and were used more by boys than by girls when evaluating exclusion. The results are discussed in terms of exclusion, development, and culture.
Petitions: Different Dimensions of Voice and Influence in the Scottish Parliament and the National Assembly for Wales
Authors: Bochel Catherine
Published: February 2012

The creation of the National Assembly for Wales and the Scottish Parliament not only saw a shift in responsibility and democratic accountability for many areas of policy, including significant areas of social policy, but also provided the opportunity for the Parliament and the Assembly to adopt ‘transformative reforms designed to expand the opportunities for citizens to connect with their governments’ (Carman 2006: 4). One such reform, which was associated with aims of increased access and openness, was the introduction of petitions systems in the new legislatures.

Drawing on case studies from the devolved level, this article explores one of the less researched non‐traditional forms of participation to examine how and what petitions can contribute to social policy. In particular, it seeks to explore the extent to which petitions systems challenge or replicate existing inequalities; what voices and interests they enable to be heard; and what impact they can have on social policy and social policies.
GRAPHICAL MODELS FOR CORRELATED DEFAULTS
Authors: Filiz Ismail Onur , Guo Xin , Morton Jason , Sturmfels Bernd
Published: February 2012

A simple graphical model for correlated defaults is proposed, with explicit formulas for the loss distribution. Algebraic geometry techniques are employed to show that this model is well posed for default dependence: it represents any given marginal distribution for single firms and pairwise correlation matrix. These techniques also provide a calibration algorithm based on maximum likelihood estimation. Finally, the model is compared with standard normal copula model in terms of tails of the loss distribution and implied correlation smile.
POPULATION AND THE ECONOMY DURING THE DEMOGRAPHIC TRANSITION
Authors: Reher David
Published: February 2012

The changes in population structure currently taking place in both developed and less‐developed nations are part of a very long‐term trend of demographic change that has yet to run its full course. The starting point of this trend is the complete rearrangement of demographic regimes characterised by significant declines in mortality coupled with widespread fertility control. This process started in a small group of European and non‐European societies during the nineteenth century and by the second half of the twentieth century had spread to much of the world. It has brought with it significant economic and social implications for societies affected which have differed by the timing of the transition but not in their basic thrust. Eventually the demographic transition promises to bring with it very rapid and widespread ageing and, within a few decades, world population decline. Some of the long‐term economic implications of this entire process are discussed in this article.
SIR WALDRON SMITHERS AND THE LONG WALK TO FINCHLEY
Authors: Farrant Andrew , Tynan Nicola
Published: February 2012

The television drama ‘Margaret Thatcher: The Long Walk to Finchley’ has Sir Waldron Smithers strongly objecting to Thatcher's selection as a Conservative candidate prior to the 1950 General Election. It is more likely that Smithers would have found her a kindred ideological spirit: both shared an anti‐socialist commitment and admiration for Hayek's ‘The Road to Serfdom’.
PRICE EFFECTS OF SHOPPING HOURS REGULATION: EVIDENCE FROM GERMANY
Authors: Reddy Karthik
Published: February 2012

This article investigates the price effects of shopping hours legislation in order to evaluate empirically the theoretical argument that such regulations protect consumers from price increases. The paper first provides a review of the literature; it then analyses the data prior to and following the liberalisation of German shopping hours regulations in 2006 and 2007 in order to estimate the effects of these changes. The article finds that liberalisation resulted in a fall in prices. This conclusion adds to a growing body of literature suggesting that shopping hours regulations entail significant economic costs.
COUNTERING THE ASSAULT ON CAPITALISM
Authors: Smith, Jr. Fred L.
Published: February 2012

Capitalism is the most efficient system for solving problems and for advancing human welfare. Yet it faces opposition both from intellectuals and those with vested interests in big government. If business leaders would push for ‘liberate to stimulate policies’, they might succeed in creating a freer tomorrow and solving more of humanity's problems.
PROBLEMS OF PUBLIC HIGHER EDUCATION IN THE USA: CAUSES AND CONSEQUENCES
Authors: Murchison William , Pejovich Svetozar
Published: February 2012

High costs and low graduation rates characteristic of 21st‐century US public higher education stem from the bout of rent‐seeking attributable to the post‐Sputnik explosion in research spending and the consequent crusade to enrol new students, with diminishing concern for academic aptitude. New policies that tighten admission standards, encourage earlier graduation and enhance financial aid for the truly needy would constructively address these problems, as would incentives for faculty members to curtail outside consulting.
Dynamic Optimal Pension Fund Portfolios when Risk Preferences Are Heterogeneous among Pension Participants
Authors: Honda Toshiki
Published: February 2012

In this paper, we consider the problem of an optimal pension fund portfolio given the heterogeneous risk preferences of pension fund participants. The relative risk aversion of a pension fund tends to be a decreasing function of the level of aggregate wealth. We find that the dynamic optimal portfolio is simply characterized as the weighted sum of the optimal portfolio for each participant. Our model helps successfully establish the microfoundation of asset liability management models. A numerical example using recent Japanese data indicates the significant total welfare losses of adopting a suboptimal portfolio strategy and an inefficient risk‐sharing rule.
Neoliberalism, policy localisation and idealised subjects: a case study on educational restructuring in England
Authors: Holloway Sarah L , Pimlott‐Wilson Helena
Published: February 2012

Debate about neoliberalism has been a significant feature of twenty‐first century geography. Appreciation of the contingent nature of neoliberalisation has promoted interest in the localisation of policy, and this paper furthers debate in three ways. First, it highlights the importance of the peopling of the state and more specifically the importance of everyday public sector workers in the localised production of roll‐out neoliberalisation. Second, it illustrates the significance of these actors’ ideas about idealised policy subjects – and the ways they relate these to their own client groups in different socio‐economic neighbourhoods – in the localised emergence of policy. Third, it explores the consequences of this for geographically and socially uneven service provision under neoliberalisation. These arguments are illustrated through a case study focus on educational restructuring under New Labour in England. Our focus is on the Extended Service initiative which combines workfare and family policy agendas by giving primary schools a duty to provide/signpost: wraparound childcare, enrichment activities for children, and parenting support. The case study explores how headteachers’ understandings of idealised neoliberal parenting subject positions, and their notions of ideal childhoods, shape their attitudes to the implementation of this programme in schools serving different socio‐economic communities. This process not only involves the reproduction of classed, (de)gendered, and heterosexed discourses seen in national policy, but also moments where local actors draw on alternative models of parenting and/or childhood to influence school‐based policy, with the result that what is perceived to be ‘good’ for families of one social class is not seen to be so for others. There is a complex politics at play here. Academics must expose the class biases inherent in neoliberal policies at the same time as they work as ‘critical friends’ in improving public service provision which impacts positively on some individuals’ lives.
Pattern and timing of the northwestern Barents Sea Ice Sheet deglaciation and indications of episodic Holocene deposition
Authors: Rüther Denise Christina , Bjarnadóttir Lilja Rún , Junttila Juho , Husum Katrine , Rasmussen Tine Lander , Lucchi Renata Giulia , Andreassen Karin
Published: February 2012

The origin of two acoustic sediment units has been studied based on lithological facies, chronology and benthic stable isotope values as well as on foraminifera and clay mineral assemblages in six marine sediment cores from Kveithola, a small trough west of Spitsbergenbanken on the western Barents Sea margin. We have identified four time slices with characteristic sedimentary environments. Before c. 14.2 cal. ka, rhythmically laminated muds indicate extensive sea ice cover in the area. From c. 13.9 to 14.2 cal. ka, muds rich in ice‐rafted debris were deposited during the disintegration of grounded ice on Spitsbergenbanken. From c. 10.3 to 13.1 cal. ka, sediments with heterogeneous lithologies suggest a shifting influence of suspension settling and iceberg rafting, probably derived from a decaying Barents Sea Ice Sheet in the inner‐fjord and land areas to the north of Kveithola. Holocene deposition was episodic and characterized by the deposition of calcareous sands and shell debris, indicative of strong bottom currents. We speculate that a marked erosional boundary at c. 8.2 cal. ka may have been caused by the Storegga tsunami. Whilst deposition was sparse during the Holocene, Kveithola acted as a sediment trap during the preceding deglaciation. Investigation of the deglacial sediments provides unprecedented details on the dynamics and timing of glacial retreat from Spitsbergenbanken.
Hairy Nevus Spilus: A Case Series
Authors: Singh Saurabh , Jain Naresh , Khanna Neena , Ahuja Arvind , Singh Manoj
Published: February 2012

Abstract:  Nevus spilus, also known as speckled lentiginous nevus, is a nevoid disorder characterized by hyperpigmented macules or papules scattered over a background of tan pigmentation. Although nevus spilus is mainly of cosmetic concern, malignant melanoma may rarely develop in the lesions. Although classically not mentioned as a hairy nevus, a few reports in literature mention overlying hypertrichosis in lesions of nevus spilus. We hereby report four cases of nevus spilus without malignant change with overlying terminal hairs that arose mainly from the background pigmented area.
Sporotrichosis on the Face of a 7‐Year‐Old Boy Following a Bicycle Accident
Authors: Williams Blake A. , Jennings Thomas A. , Rushing Erica C. , Wirges Marla , Russell Brian E.
Published: February 2012

Abstract:  A 7‐year‐old boy presented with an annular verrucous plaque on the chin of 5 weeks duration. The lesion occurred after a bicycle accident and was unresponsive to antibiotics. Fungal culture grew Sporothrix schenckii. Sporotrichosis should be considered and fungal culture obtained whenever a nodule or plaque fails to respond to initial treatment.
Systemic Contact Dermatitis – Kids and Ketchup
Authors: Herro Elise M. , Jacob Sharon E.
Published: February 2012

Abstract:  Systemic manifestations of allergic contact dermatitis due to consumption of foods containing balsam of Peru (Myroxylon pereirae)‐associated chemicals have recently been reported in children. We present seven children with widespread, recalcitrant dermatitis who experienced 60–80% clearance after initiating a diet low in balsam of Peru, specifically the tomato product ketchup. Furthermore, because we have observed a high prevalence of ketchup in our pediatric patients’ diets, we recommend consideration of moderate consumption of this product in patients with recalcitrant widespread dermatitis.
Multiple Pilomatricomas in Kabuki Syndrome
Authors: Hamahata Atsumori , Kamei Wataru , Ishikawa Masashi , Konoeda Hisato , Yamaki Takashi , Sakurai Hiroyuki
Published: February 2012

Abstract:  Pilomatricoma is a benign tumor of the hair matrix cell that presents predominantly in childhood. Although pilomatricoma occurs spontaneously, multiple pilomatricomas have been described in association with several inherited syndromes. We report on a 28‐year‐old man with Kabuki syndrome with three pilomatricomas in his head and thigh. Although several reports describe multiple pilomatricomas associated with Turner syndrome, there are no reports of multiple pilomatricomas combined with Kabuki syndrome. Ectodermal abnormalities such as hair abnormality and hirsutism are symptoms of Kabuki syndrome, and pilomatricomas are frequently associated with the mutations of beta‐catenin in hair follicle development. The predisposition of pilomatricomas may be not merely a coincidental finding, but an added association with Kabuki syndrome.