bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads
Authors: Kawaguchi Shuji , Iida Kei , Harada Erimi , Hanada Kousuke , Matsui Akihiro , Okamoto Masanori , Shinozaki Kazuo , Seki Motoaki , Toyoda Tetsuro 
Published: February 2012

AbstractMotivation: A reconstruction of full-length transcripts observed by next-generation sequencer or tiling arrays is an essential technique to know all phenomena of transcriptomes. Several techniques of the reconstruction have been developed. However, problems of high-level noises and biases still remain and interrupt the reconstruction. A method is required that is robust against noise and bias and correctly reconstructs transcripts regardless of equipment used.Results: We propose a completely new statistical method that reconstructs full-length transcripts and can be applied on both next-generation sequencers and tiling arrays. The method called ARTADE2 analyzes ‘positional correlation’, meaning correlations of expression values for every combination on genomic positions of multiple transcriptional data. ARTADE2 then reconstructs full-length transcripts using a logistic model based on the positional correlation and the Markov model. ARTADE2 elucidated 17 591 full-length transcripts from 55 transcriptome datasets and showed notable performance compared with other recent prediction methods. Moreover, 1489 novel transcripts were discovered. We experimentally tested 16 novel transcripts, among which 14 were confirmed by reverse transcription–polymerase chain reaction and sequence mapping. The method also showed notable performance for reconstructing of mRNA observed by a next-generation sequencer. Moreover, the positional correlation and factor analysis embedded in ARTADE2 successfully detected regions at which alternative isoforms may exist, and thus are expected to be applied for discovering transcript biomarkers for a wide range of disciplines including preemptive medicine.Availability: http://matome.base.riken.jpContact: toyoda@base.riken.jpSupplementary information: Supplementary data are available at Bioinformatics online.
Good ethics or political and cultural censoring in science?
Authors: Torrissen Ole , Glover Kevin Alan , Haug Tore , Misund Ole Arve , Skaug Hans Julius , Kaiser Matthias 
Published: February 2012

AbstractTorrissen, O., Glover, K. A., Haug, T., Misund, O. A., Skaug, H. J., and Kaiser, M. 2012. Good ethics or political and cultural censoring in science? – ICES Journal of Marine Science, 69: 493–497. Peer-reviewed journals are the cornerstones to communicating scientific results. They play a crucial role in quality assurance through the review process, but they also create opportunities for discussions in the scientific community on the implications of the results or validation of methods and data. This requires that journals adhere to commonly accepted scientific standards and are open about their editorial policy. Norwegian scientists experience problems in getting research on minke whales accepted for publication where the data have been collected in association with commercial whaling. The journal Biology Letters refuses to publish papers based on data from the Norwegian whale register while publically claiming a sole focus on scientific quality. Although there are good arguments for claiming that clearly unethical research should not be rewarded with scientific publications, one also has to realize that some fields of research are beset with unresolved ethical and cultural debates. In these cases, it is to the benefit of the progress of science, and indeed society, to be open about the issues and support arguments through scientific studies. Political or cultural censoring of scientific information will in any case jeopardize the role of journals in quality assurance of scientific research and undermine the credibility of science as a supplier of objective and reliable knowledge.
Genetic structure of the Atlantic wolffish (Anarhichas lupus L.) at Icelandic fishing grounds: another evidence of panmixia in Iceland?
Authors: Pampoulie Christophe , Skirnisdóttir Sigurlaug , Daníelsdóttir Anna Kristín , Gunnarsson Ásgeir 
Published: February 2012

AbstractPampoulie, C., Skirnisdóttir, S., Daníelsdóttir, A. K., and Gunnarsson, Á. 2012. Genetic structure of the Atlantic wolffish (Anarhichas lupus L.) at Icelandic fishing grounds: another evidence of panmixia in Iceland? – ICES Journal of Marine Science, 69: 508–515. The stock structure of the Atlantic wolffish was investigated at Icelandic fishing grounds, using 16 microsatellite loci. Despite the potential of the Atlantic wolffish to exhibit genetic structure (lack of eggs/larval dispersal and adults are sedentary), none of the genetic tests applied in this study detected significant genetic differentiation among the contemporary samples as well as among the contemporary and archived samples. The results of this study therefore suggested a lack of genetic structure among the populations of Atlantic wolffish in Icelandic waters and temporal stability over a period of ∼10 years. These results are discussed in terms of biological characteristics of Atlantic wolffish, recent isolation of populations, and their application to sustainable fisheries management issues.
British Idealism
Authors: Brooks Thom 
Published: February 2012

British idealism flourished in the late nineteenth and early twentieth centuries. It was a movement with a lasting influence on the social and political thought of its time in particular. British idealists helped popularize the work of Immanuel Kant and G. W. F. Hegel in the anglophone world, but they also sought to use insights from the philosophies of Kant and Hegel to help create a new idealism to address the many pressing issues of the Victorian period in Britain and its aftermath. These contributions related to theories of freedom, the common good, political obligation, the state, and punishment. The British idealists also made important contributions in areas other than Hegelian scholarship and ethics, including logic, metaphysics, and the philosophy of religion. The movement declined by the start of World War I. This entry will highlight the most important work by British idealists themselves and by their best interpreters. Thus this entry will be grouped by individuals rather than by theme.
Photosynthetic Pigment Localization and Thylakoid Membrane Morphology Are Altered in Synechocystis 6803 Phycobilisome Mutants
Authors: Collins Aaron M. , Liberton Michelle , Jones Howland D.T. , Garcia Omar F. , Pakrasi Himadri B. , Timlin Jerilyn A. 
Published: February 2012

Abstract
Cyanobacteria are oxygenic photosynthetic prokaryotes that are the progenitors of the chloroplasts of algae and plants. These organisms harvest light using large membrane-extrinsic phycobilisome antenna in addition to membrane-bound chlorophyll-containing proteins. Similar to eukaryotic photosynthetic organisms, cyanobacteria possess thylakoid membranes that house photosystem (PS) I and PSII, which drive the oxidation of water and the reduction of NADP+, respectively. While thylakoid morphology has been studied in some strains of cyanobacteria, the global distribution of PSI and PSII within the thylakoid membrane and the corresponding location of the light-harvesting phycobilisomes are not known in detail, and such information is required to understand the functioning of cyanobacterial photosynthesis on a larger scale. Here, we have addressed this question using a combination of electron microscopy and hyperspectral confocal fluorescence microscopy in wild-type Synechocystis species PCC 6803 and a series of mutants in which phycobilisomes are progressively truncated. We show that as the phycobilisome antenna is diminished, large-scale changes in thylakoid morphology are observed, accompanied by increased physical segregation of the two photosystems. Finally, we quantified the emission intensities originating from the two photosystems in vivo on a per cell basis to show that the PSI:PSII ratio is progressively decreased in the mutants. This results from both an increase in the amount of photosystem II and a decrease in the photosystem I concentration. We propose that these changes are an adaptive strategy that allows cells to balance the light absorption capabilities of photosystems I and II under light-limiting conditions.
Systematic review of international evidence on the effectiveness and costs of paediatric home care for children and young people who are ill
Authors: Parker G. , Spiers G. , Gridley K. , Atkin K. , Birks Y. , Lowson K. , Light K. 
Published: February 2012

AbstractPromoting ‘care closer to home’ for ill children is a policy and practice objective internationally. Progress towards this goal is hampered by a perceived lack of evidence on effectiveness and costs. The aim of the work reported here was to establish the strength of current international evidence on the effectiveness and costs of paediatric home care by updating and extending an earlier systematic review. A systematic review following Centre for Reviews and Dissemination guidelines involved updating electronic searches, and extending them to cover paediatric home care for short‐term acute conditions. Twenty‐one databases were searched from 1990 to April 2007. Hand searching was also carried out. Pairs of team members, guided by an algorithm, selected randomized controlled trials (RCTs), other comparative studies and studies including health economics data. A third reviewer resolved any disagreements. The quality of RCTs was assessed, but a ‘best‐evidence’ approach was taken overall. Data were extracted into specifically designed spreadsheets and a second team member checked all data. Narrative synthesis was used throughout. This paper reports findings from RCTs and studies with health economics data. In total, 16 570 publications were identified after de‐duplication. Eleven new RCTs (reported in 17 papers) and 20 papers with health economics data were included and reviewed. Evidence on costs and effectiveness of paediatric home care has not grown substantially since the previous review, but this updated review adds weight to the conclusion that it can deliver equivalent clinical outcomes for children and not impose a greater burden on families. Indeed, in some cases, there is evidence of reduced burden and costs for families compared with hospital care. There is also growing evidence, albeit based on weaker evidence, that paediatric home care may reduce costs for health services, particularly for children with complex and long‐term needs.
Dental admissions in children under two years – a total‐population investigation
Authors: Slack‐Smith L. , Colvin L. , Leonard H. , Kilpatrick N. , Read A. , Messer L. B. 
Published: February 2012

AbstractBackground  There is a lack of literature describing dental admissions in children particularly very young children. This paper describes dental and oral cavity admissions and associated factors in children under two years of age using total‐population databases.Methods  The data used for this study were extracted from population‐based databases which are linkable with midwives' data collected on all births in Western Australia. Children born from 1980 to 1998 inclusive (n= 459 831) were followed until two years of age including data on deaths, hospital admissions, birth defects and intellectual disability. Dental admissions (by ICD‐9 category) and associated factors were investigated.Results  There were 1513 dental admissions occurring in 1459 of the children up to the age of two years. Children were most frequently admitted under ICD‐9 category 521, which includes a hospital admission for dental caries (39% of all oral cavity admissions), followed by ICD‐9 category 528 (29%), which includes diseases of the oral soft tissues. Univariate analysis indicated that those with intellectual disability (OR 2.10, 95%CI 1.40–3.16), birth defect (1.74, 1.45–2.09), residing in a region without fluoridated water (2.15, 1.72–2.69) being male (1.14, 1.03–1.26), those from rural areas (2.29, 2.07–2.54) and Indigenous children (4.45, 3.91–5.05) were significantly more likely to have had a dental admission.Conclusion  Using total‐population data allowed us to describe the admissions in children under two years and associated factors while able to identify children with intellectual disability or birth defects.
Eosinophil peroxidase induces the expression and function of acid‐sensing ion channel‐3 in allergic rhinitis: in vitro evidence in cultured epithelial cells
Authors: G. Khoo S. , Al‐Alawi M. , Walsh M. T. , Hennigan K. , Glynn S. , Thornton M. , McQuaid S. , Wang Y. , Hamilton P. W. , Verriere V. , Gleich G. J. , Harvey B. J. , Costello R. W. , McGarvey L. P. 
Published: February 2012

SummaryBackgroundAcid‐sensing ion channels (ASIC) are a family of acid‐activated ligand‐gated cation channels. As tissue acidosis is a feature of inflammatory conditions, such as allergic rhinitis (AR), we investigated the expression and function of these channels in AR.ObjectivesThe aim of the study was to assess expression and function of ASIC channels in the nasal mucosa of control and AR subjects.MethodsImmunohistochemical localization of ASIC receptors and functional responses to lactic acid application were investigated. In vitro studies on cultured epithelial cells were performed to assess underlying mechanisms of ASIC function.ResultsLactic acid at pH 7.03 induced a significant rise in nasal fluid secretion that was inhibited by pre‐treatment with the ASIC inhibitor amiloride in AR subjects (n = 19). Quantitative PCR on cDNA isolated from nasal biopsies from control and AR subjects demonstrated that ASIC‐1 was equally expressed in both populations, but ASIC‐3 was significantly more highly expressed in AR (P < 0.02). Immunohistochemistry confirmed significantly higher ASIC‐3 protein expression on nasal epithelial cells in AR patients than controls (P < 0.01). Immunoreactivity for EPO+ eosinophils in both nasal epithelium and submucosa was more prominent in AR compared with controls. A mechanism of induction of ASIC‐3 expression relevant to AR was suggested by the finding that eosinophil peroxidase (EPO), acting via ERK1/2, induced the expression of ASIC‐3 in epithelial cells. Furthermore, using a quantitative functional measure of epithelial cell secretory function in vitro, EPO increased the air‐surface liquid depth via an ASIC‐dependent chloride secretory pathway.ConclusionsThis data suggests a possible mechanism for the observed association of eosinophils and rhinorrhoea in AR and is manifested through enhanced ASIC‐3 expression.
Hepatotoxicity and cutaneous reactions after antithyroid drug administration
Authors: Otsuka Fumiko , Noh Jaeduk Y. , Chino Toshiko , Shimizu Taeko , Mukasa Koji , Ito Kunihiko , Ito Koichi , Taniyama Matsuo 
Published: February 2012

SummaryObjectiveUse of the antithyroid drugs (ATDs) thiamazole (MMI) and propylthiouracil (PTU) is associated with a high frequency of side effects. When patients experience side effects with one (the 1st) ATD, it is usually discontinued and another is administered (the 2nd ATD). We investigated side effects associated with the 1st and 2nd ATDs.Design and PatientsFour hundred forty‐nine patients with untreated Graves' disease (GD) were randomly assigned to three groups according to ATD type and/or dosage: 15 mg/day MMI, 30 mg/day MMI and 300 mg/day PTU. The type, frequency and onset of side effects were assessed. We also studied the side effects associated with the 2nd ATD after cessation of the 1st ATD.MeasurementsCutaneous reactions, liver dysfunction and other side effects were examined every 2 weeks after starting ATD administration.ResultsThe overall frequency of side effects in patients taking 15 mg/day MMI was low. The frequencies of cutaneous reactions in patients taking 30 mg/day MMI and hepatotoxicity in those taking 300 mg/day PTU were high. Hepatotoxicity developed later than cutaneous reactions with PTU. Hepatotoxicity developed earlier in the 30 mg/day MMI group than in the other two groups. The frequency of side effects did not differ between the 2nd and 1st ATDs. Hepatotoxicity occurred at a higher frequency in patients who were switched from MMI to PTU because of hepatotoxicity of the former.ConclusionAttention to the onset times of side effects and cross‐reactivity of ATDs can lead to safer treatment of GD.
Diagnostic value of urine erythrocyte morphology in the detection of glomerular disease in SurePath™ liquid‐based cytology compared with fresh urine sediment examination
Authors: Ohsaki H. , Hirouchi T. , Hayashi N. , Okanoue E. , Ohara M. , Kuroda N. , Hirakawa E. , Norimatsu Y. 
Published: February 2012

H. Ohsaki, T. Hirouchi, N. Hayashi, E. Okanoue, M. Ohara, N. Kuroda, E. Hirakawa and Y. Norimatsu  Diagnostic value of urine erythrocyte morphology in the detection of glomerular disease in SurePath™ liquid‐based cytology compared with fresh urine sediment examinationObjective:  To assess whether the morphology of urine erythrocytes can be an effective tool for distinguishing glomerular disease from lower urinary tract disease in SurePath™ liquid‐based cytology (SP‐LBC).Methods:  We examined four morphological parameters of erythrocytes: (1) irregular erythrocytes (of all types including fragmented forms) comprising greater than or equal to 20% of erythrocytes; (2) uniform erythrocytes (>80%); (3) doughnut or target‐like shaped (D/T) erythrocytes (≥1%); and (4) acanthocytes (≥1%) in glomerular disease (n = 32) and lower urinary tract disease (n = 20) with SP‐LBC slides in cases that had also been assessed by fresh urine sediment examination.Results:  Sensitivity of D/T erythrocytes and acanthocytes (dysmorphic erythrocytes) for glomerular disease were 100% and 87.5%, respectively, with urine sediment examination, and 81.3% and 46.9%, respectively, in SP‐LBC slides. Specificity was 100% for D/T erythrocytes and acanthocytes using either procedure. While irregular erythrocytes were specific for glomerular disease using urine sediment examination, they were seen in 70% of those with lower urinary tract disease using SP‐LBC slides as a result of the deformation of erythrocytes by the fixative.Conclusions:  Although the sensitivity of D/T erythrocytes and acanthocytes for glomerular disease was lower in SP‐LBC slides than fresh urine sediment examination, their specificity was equally high. Therefore, urine erythrocyte morphology is useful in the detection of glomerular disease with the SP‐LBC slides. However, morphological features apart from D/T erythrocytes and acanthocytes are not useful in SP‐LBC slides.
Geostatistical traveltime tomography in elliptically anisotropic media
Authors: Giroux Bernard , Gloaguen Erwan 
Published: February 2012

ABSTRACTIn geological materials, anisotropy may arise due to different mechanisms and can be found at different scales. Neglecting anisotropy in traveltime tomographic reconstruction leads to artefacts that can obscure important subsurface features. In this paper, a geostatistical tomography algorithm to invert cross‐hole traveltime data in elliptically anisotropic media is presented. The advantages of geostatistical tomography are that the solution is regularized by the covariance of the model parameters, that known model parameters can be used as constraints and fitted exactly or within a prescribed variance and that stochastic simulations can be performed to appraise the variability of the solution space. The benefits of the algorithm to image anisotropic media are illustrated by two examples using synthetic georadar data and real seismic data. The first example confirms suspected electromagnetic anisotropy in the vadose zone caused by relatively rapid water content variations with respect to wavelength at georadar frequencies. The second presents how sonic log data can be used to constrain the inversion of cross‐well seismic data and how geostatistical simulations can be used to infer parameter uncertainty. Results of both examples show that considering anisotropy yields a better fit to the data at high ray angles and reduces reconstruction artefacts.
A hybrid absorbing boundary condition for elastic staggered‐grid modelling
Authors: Liu Yang , Sen Mrinal K. 
Published: February 2012

ABSTRACTWe recently proposed an efficient hybrid scheme to absorb boundary reflections for acoustic wave modelling that could attain nearly perfect absorptions. This scheme uses weighted averaging of wavefields in a transition area, between the inner area and the model boundaries. In this paper we report on the extension of this scheme to 2D elastic wave modelling with displacement‐stress formulations on staggered grids using explicit finite‐difference, pseudo‐implicit finite‐difference and pseudo‐spectral methods. Numerical modelling results of elastic wave equations with hybrid absorbing boundary conditions show great improvement for modelling stability and significant absorption for boundary reflections, compared with the conventional Higdon absorbing boundary conditions, demonstrating the effectiveness of this scheme for elastic wave modelling. The modelling results also show that the hybrid scheme works well in 2D rotated staggered‐grid modelling for isotropic medium, 2D staggered‐grid modelling for vertically transversely isotropic medium and 2D rotated staggered‐grid modelling for tilted transversely isotropic medium.
Biomass and tiller growth responses to competition between Ky31 and MaxQ Festuca arundinacea cultivars and response of Ky31 to exogenously applied liquid preparation of Neotyphodium coenophialum under glasshouse conditions
Authors: Mersch S. M. , Cahoon A. B. 
Published: February 2012

AbstractTall fescue (Festuca arundinacea) forms a mutualistic symbiosis with the fungal endophyte Neotyphodium coenophialum which produces ergot alkaloids toxic to grazing animals. One approach to reduce pathological effects has been to introduce an exotic endophyte that does not produce toxic compounds yet still confers host‐plant benefits. We measured biomass accumulation and competition between two tall fescue cultivars with different endophytes grown in close proximity and tested if compounds from endophytes can diffuse from one plant to another. Ky31 (tall fescue with natural endophyte) and MaxQ (tall fescue with introduced exotic endophyte) were grown separately and together in a pot experiment under greenhouse conditions. The cultivars had comparable biomass production in monoculture, but when grown in mixed‐culture MaxQ had a significantly lower tiller number (2.92 ± 0.15 tillers/plant) and size (0.048 g ± 0.003) than Ky31 (4.06 ± 0.16 tillers/plant) (0.072 ± 0.002 g). Aqueous endophyte preparations were made and applied topically to E+ and E‐ Ky31. E‐ plants receiving doses of this preparation produced significantly more tillers (3 ± 0.18 tillers/plant) and larger tillers (0.074 ± 0.006 g) than untreated control plants (2.2 ± 0.13 tillers/plant) (0.0428 ± 0.0072 g). These observations suggested that a diffusible compound might induce a growth benefit conferred by the tall fescue endophyte.