bluuebunny/crossref_metadata_2025_split huggingface dataset:
Planetary Nebulae: Observational Properties, Mimics and Diagnostics
Authors: Frew David J. , Parker Quentin A. 
Published: May 2010

AbstractThe total number of true, likely and possible planetary nebulae (PN) now known in the Milky Way is nearly 3000, double the number known a decade ago. The new discoveries are a legacy of the recent availability of wide field, narrowband imaging surveys, primarily in the light of H-alpha. In this paper, we summarise the various PN discovery techniques, and give an overview of the many types of objects which mimic PN and which appear as contaminants in both Galactic and extragalactic samples. Much improved discrimination of classical PN from their mimics is now possible based on the wide variety of high-quality multiwavelength data sets that are now available. We offer improved taxonomic and observational definitions for the PN phenomenon based on evaluation of these better diagnostic capabilities. However, we note that evidence is increasing that the PN phenomenon is heterogeneous, and PN are likely to be formed from multiple evolutionary scenarios. In particular, the relationships between some collimated symbiotic outflows and bipolar PN remain uncertain.
An Evaluation of the Excitation-Class Parameter for the Central Stars of Planetary Nebulae
Authors: Reid Warren A. , Parker Quentin A. 
Published: May 2010

AbstractThe three main methods currently in use for estimating the excitation class of planetary nebulae (PNe) central stars are compared and evaluated using 586 newly discovered and previously known PNe in the Large Magellanic Cloud (LMC). In order to achieve this we ran a series of evaluation tests using line ratios derived from de-reddened, flux-calibrated spectra. Pronounced differences between the methods are exposed after comparing the distribution of objects to their derived excitation. Line ratio comparisons show that each method's input parameters have a strong effect on the estimated excitation of a central star. Diagrams were created by comparing excitation classes with Hβ line fluxes. The best methods are then compared to published temperatures using the Zanstra method and assessed for their ability to reflect central star effective temperatures and evolution. As a result we call for a clarification of the term ‘excitation class’ according to the different input parameters used. The first method, which we refer to as Exneb relies purely on the ratios of certain key emission lines. The second method, which we refer to as Ex* includes modeling to create a continuous variable and, for optically thick PNe in the Magellanic Clouds, is designed to relate more closely to intrinsic stellar parameters. The third method, we refer to as Ex[Oiii]/Hβ since the [Oiii]/Hβ ratio is used in isolation to other temperature diagnostics. Each of these methods is shown to have serious drawbacks when used as an indicator for central star temperature. Finally, we suggest a new method (Exρ) for estimating excitation class incorporating both the [Oiii]/Hβ and the HeII λ4686/Hβ ratios. Although any attempt to provide accurate central star temperatures using the excitation class derived from nebula lines will always be limited, we show that this new method provides a substantial improvement over previous methods with better agreement to temperatures derived through the Zanstra method.
CisGenome Browser: a flexible tool for genomic data visualization
Authors: Jiang Hui , Wang Fan , Dyer Nigel P. , Wong Wing Hung 
Published: June 2010

Abstract
Summary: We present an open source, platform independent tool, called CisGenome Browser, which can work together with any other data analysis program to serve as a flexible component for genomic data visualization. It can also work by itself as a standalone genome browser. By working as a light-weight web server, CisGenome Browser is a convenient tool for data sharing between labs. It has features that are specifically designed for ultra high-throughput sequencing data visualization.
Availability: http://biogibbs.stanford.edu/∼jiangh/browser/
Contact: jiangh@stanford.edu
Purification of RNA by SDS Solubilization and Phenol Extraction
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W. 
Published: June 2010

INTRODUCTIONThis protocol describes a method for RNA purification by sodium dodecyl sulfate (SDS) solubilization and phenol extraction. It is of wide utility and is used routinely to deproteinize RNAs in biological material that has been solubilized in SDS, an ionic detergent that dissolves membranes, disrupts protein-nucleic acid interactions, and inactivates ribonucleases. Once solubilized, addition of phenol or phenol:chloroform:isoamyl alcohol (PCA) completely denatures the protein, and it becomes insoluble in aqueous solution. PCA extraction is the method of choice for preparing cytoplasmic RNA from tissue culture cells or in any other situation (e.g., enzyme reactions) where solubilization in SDS is easily achievable.
Removal of Ribosomal Subunits (and rRNA) from Cytoplasmic Extracts before Solubilization with SDS and Deproteinization
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W. 
Published: June 2010

INTRODUCTIONMore than 95% of total RNA is composed of ribosomal RNAs (rRNAs) (28S, 18S, 5.8S, and 5S). Here, we present a method that is effective in removing rRNA before extraction and purification of total RNA. If you choose to prepare cytoplasmic RNA and wish to analyze any RNA other than rRNA, it is desirable to eliminate the rRNAs by taking advantage of the fact that the ribosomal subunits are very large (40S and 60S). Few, if any, other cellular RNAs are present in such large macromolecular complexes. The vast majority of rRNAs can be removed by sedimentation. Of course, steps must be taken to avoid co-sedimentation of desired RNAs. Co-sedimentation can be greatly reduced by first dissociating ribosomes into their respective subunits by EDTA treatment. The subunits are then “cleaned” by treatment with high salt and nonionic detergent. Ribosomal subunits remain intact under these conditions and can be sedimented free of other RNAs. Subsequently, the remaining RNAs (messenger RNAs [mRNAs] and all other RNAs) can be purified and analyzed by a variety of methods.
Removal of DNA from RNA
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W. 
Published: June 2010

INTRODUCTIONDNA contamination of RNA preparations can present significant problems, especially for polymerase chain reaction (PCR)-based applications. No RNA extraction procedure excludes DNA entirely. Cytoplasmic RNA can be contaminated with DNA because of nuclei breakage during preparation. Moreover, TRIzol preparations do not exclude plasmids or other small DNA fragments. This article describes the reliable and effective method of eliminating DNA from RNA preparations via DNase digestion. DNase I specifically digests DNA into small oligonucleotides, leaving RNA intact.
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
Authors: Meyer Matthias , Kircher Martin 
Published: June 2010

INTRODUCTIONThe large amount of DNA sequence data generated by high-throughput sequencing technologies often allows multiple samples to be sequenced in parallel on a single sequencing run. This is particularly true if subsets of the genome are studied rather than complete genomes. In recent years, target capture from sequencing libraries has largely replaced polymerase chain reaction (PCR) as the preferred method of target enrichment. Parallelizing target capture and sequencing for multiple samples requires the incorporation of sample-specific barcodes into sequencing libraries, which is necessary to trace back the sample source of each sequence. This protocol describes a fast and reliable method for the preparation of barcoded (“indexed”) sequencing libraries for Illumina’s Genome Analyzer platform. The protocol avoids expensive commercial library preparation kits and can be performed in a 96-well plate setup using multi-channel pipettes, requiring not more than two or three days of lab work. Libraries can be prepared from any type of double-stranded DNA, even if present in subnanogram quantity.
Tracking and Quantitative Analysis of Dynamic Movements of Cells and Particles
Authors: Rohr Karl , Godinez William J. , Harder Nathalie , Wörz Stefan , Mattes Julian , Tvaruskó Wolfgang , Eils Roland 
Published: June 2010

INTRODUCTIONUnderstanding complex cellular processes requires investigating the underlying mechanisms within a spatiotemporal context. Although cellular processes are dynamic in nature, most studies in molecular cell biology are based on fixed specimens, for example, using immunocytochemistry or fluorescence in situ hybridization (FISH). However, breakthroughs in fluorescence microscopy imaging techniques, in particular, the discovery of green fluorescent protein (GFP) and its spectral variants, have facilitated the study of a wide range of dynamic processes by allowing nondestructive labeling of target structures in living cells. In addition, the tremendous improvements in spatial and temporal resolution of light microscopes now allow cellular processes to be analyzed in unprecedented detail. These state-of-the-art imaging technologies, however, provide a huge amount of digital image data. To cope with the enormous amount of image data and to extract reproducible as well as quantitative information, computer-based image analysis is required. In this article, we describe methods for computer-based analysis of multidimensional live cell microscopy images and their application to study the dynamics of cells and particles. First, we sketch a general workflow for quantitative analysis of live cell images. Then, we detail computational methods for automatic image analysis comprising image preprocessing, segmentation, registration, tracking, and classification. We conclude with a discussion of quantitative analysis and systems biology.
Meta-Analysis of Genome-Wide Association Studies
Authors: de Bakker Paul I.W. , Neale Benjamin M. , Daly Mark J. 
Published: June 2010

INTRODUCTIONIndividual genome-wide association studies have only limited power to find novel loci underlying complex traits and common diseases. With relatively modest sample and effect sizes, a true association between genotype and phenotype may never meet genome-wide statistical significance (P < 5 × 10-8) in a single study. Through meta-analysis, novel susceptibility loci can be discovered by effectively summing the statistical evidence of individually underpowered studies. Most genetic discoveries for complex traits are now made through meta-analysis collaborations, which so far have been restricted to single-locus analyses, testing for main effects at a single polymorphism at a time. A key benefit of this approach is that individual-level genotype (and phenotype) data do not need to be exchanged between research groups. In this article, we focus on meta-analysis at individual single-nucleotide polymorphisms (SNPs), paying particular attention to how imputation uncertainty can be incorporated into the association analysis and subsequent meta-analysis. Probably the most important aspect of genome-wide association meta-analysis is harmonization of the study results. As studies differ in design, sample collection, genotyping platforms, and association analysis methods, it is important that the association results (per SNP) of each study can be formatted, exchanged, and analyzed in such a way that the statistical evidence can be combined appropriately and that no valuable information is lost. Without minimizing the importance of having a clear phenotype definition (and corresponding measurements), we will assume that investigators representing the various studies have made sensible agreements about phenotype definitions, necessary sample exclusions, and appropriate covariate modeling.
Clinical course of guttate psoriasis: Long‐term follow‐up study
Authors: KO Hyun‐Chang , JWA Seung‐Wook , SONG Margaret , KIM Moon‐Bum , KWON Kyung‐Sool 
Published: June 2010

AbstractGuttate psoriasis, known to have a better prognosis than other types of psoriasis, shows rapid involution and longer remission, but its clinical course has barely been studied. The aim of this study was to determine the clinical course and to compare the clinical and laboratory features of guttate psoriasis. This is a retrospective study of 26 patients with guttate psoriasis. The patients were divided into two groups; the good one with complete remission and long remission for at least 1 year (group A) and the poor one with incomplete remission and progression into chronic plaque psoriasis (group B). Among 36 patients, 22 patients (61.1%) were group A and 14 patients (38.9%) were group B. In group A, most of the skin lesions disappeared within 8 months. In group B, two patients without proper treatment progressed to plaque psoriasis. The onset age was younger and more frequent upper respiratory infection and high anti‐streptolysin O (ASO) titer were found in group A, but family history of psoriasis was more common in group B. Patients had two distingushable clinical courses: rapid involuting course with long‐term remission and chronic course without remission. There was a tendency toward younger age of onset with elevated ASO titer in patients with rapid involuting course.
Immunoglobulin G‐dependent changes in basophil allergen threshold sensitivity during birch pollen immunotherapy
Authors: Lalek N. , Kosnik M. , Silar M. , Korosec P. 
Published: May 2010

SummaryBackground
The effects of pollen immunotherapy on effector cells of allergic inflammation, such as mast cells and basophils, are poorly understood.Objective
For this reason, we conducted an open study on basophil allergen threshold sensitivity during birch pollen immunotherapy.Methods
Basophil sensitivity was measured by CD63 flow cytometry in 14 patients with moderate–severe intermittent birch pollen rhinitis using four log allergen concentrations. In nine patients, we analysed the basophil sensitivity before and during treatment with subcutaneous birch immunotherapy (perennial scheme with allergoid). We also included eight birch‐allergic donor subjects for IgG inhibition experiments and eight control subjects.Results
There was a decrease in basophil allergen threshold sensitivity after 2, 3, and 5 months of immunotherapy. This decrease was correlated with an improvement in patients' symptoms measured on a visual analogue scale. The serum obtained after immunotherapy induced a significant decrease in allergen threshold sensitivity in donor birch‐allergic basophils. This inhibition was not observed after IgG depletion from the serum.Conclusions
In this study, we showed that birch immunotherapy‐induced IgG antibodies are associated with a reduction in basophil allergen threshold sensitivity. Further studies are needed to show whether the changes in basophil sensitivity are of clinical relevance in pollen immunotherapy. Cite this as: N. Lalek, M. Kosnik, M. Silar and P. Korosec, Clinical & Experimental Allergy, 2010 (40) 1186–1193.
Nuclear fluorescence serum reactivity on monkey oesophagus: a new antibody for the follow-up of coeliac disease?
Authors: Picarelli A , Sabbatella L , Di Tola M , Silano M , Nicolussi A , D'Inzeo S , Coppa A 
Published: May 2010

Summary
We have identified previously a nuclear fluorescence reactivity (NFR) pattern on monkey oesophagus sections exposed to coeliac disease (CD) patients' sera positive for anti-endomysium antibodies (EMA). The aim of the present work was to characterize the NFR, study the time–course of NFR-positive results in relation to gluten withdrawal and evaluate the potential role of NFR in the follow-up of CD. Twenty untreated, 87 treated CD patients and 15 healthy controls were recruited and followed for 12 months. Their sera were incubated on monkey oesophagus sections to evaluate the presence of NFR by indirect immunofluorescence analysis. Duodenal mucosa samples from treated CD patients were challenged with gliadin peptides, and thus the occurrence of NFR in culture supernatants was assessed. The NFR immunoglobulins (Igs) reactivity with the nuclear extract of a human intestinal cell line was investigated. Serum NFR was present in all untreated CD patients, persisted up to 151 ± 37 days from gluten withdrawal and reappeared in treated CD patients under dietary transgressions. Serum NFR was also detected in two healthy controls. In culture supernatants of coeliac intestinal mucosa challenged with gliadin peptides, NFR appeared before EMA. The Igs responsible for NFR were identified as belonging to the IgA2 subclass. The NFR resulted differently from EMA and anti-nuclear antibodies, but reacted with two nuclear antigens of 65 and 49 kDa. A new autoantibody, named NFR related to CD, was described. Furthermore, NFR detection might become a valuable tool in monitoring adherence to a gluten-free diet and identifying slight dietary transgressions.
Rituximab treatment in patients with active Graves' orbitopathy: effects on proinflammatory and humoral immune reactions
Authors: Vannucchi G , Campi I , Bonomi M , Covelli D , Dazzi D , Currò N , Simonetta S , Bonara P , Persani L , Guastella C , Wall J , Beck-Peccoz P , Salvi M 
Published: May 2010

Summary
In active Graves' orbitopathy (GO), proinflammatory cytokines predominate. Circulating thyroid stimulating hormone (TSH)-receptor antibodies (TRAb) have been correlated with GO clinical activity and severity. In preliminary studies rituximab (RTX), an anti-CD 20 monoclonal antibody, has induced clinical improvement of active GO without a change in serum anti-thyroid antibodies. We have studied whether RTX in GO acts by affecting proinflammatory cytokines and thyroid and orbital-directed antibodies. Ten patients with GO were treated with RTX, administered twice intravenously (i.v.) (1000 mg) at days 1 and 15, and 20 with methylprednisolone, administered weekly i.v. (500 mg), for 16 weeks. Patients were studied before treatment, at B cell depletion and at 4, 8, 16, 20, 30 and 50 weeks. Peripheral lymphocytes, serum interleukin (sIL)-6, sIL-6r, chemokine (C-X-C motif) ligand 10 (CXCL10), TRAb and stimulating antibodies (TSAb) and autoantibodies against orbital calsequestrin, collagen XIII and flavoprotein subunit of succinate dehydrogenase (FP-SDH) were measured at baseline and after treatment. Serum IL-6 and sIL-6R concentrations did not change after RTX [P = not significant (n.s.)]. Serum CXCL10 increased after RTX at B cell depletion and at 30 weeks (P &lt; 0·003). Serum TSAb did not change in relation to TRAb, nor did antibodies against orbital antigens (P = n.s.). In conclusion, this study shows that RTX in GO does not affect humoral reactions. The observed increase of serum CXCL10 concentrations at B cell depletion may result from cell lysis. We suggest that RTX may exert its effect in GO by inhibiting B cell antigen presentation.
Immunotherapy prospects for acute myeloid leukaemia
Authors: Barrett A J , Le Blanc K 
Published: May 2010

Summary
While chemotherapy is successful at inducing remission of acute myeloid leukaemia (AML), the disease has a high probability of relapse. Strategies to prevent relapse involve consolidation chemotherapy, stem cell transplantation and immunotherapy. Evidence for immunosurveillance of AML and susceptibility of leukaemia cells to both T cell and natural killer (NK) cell attack and justifies the application of immune strategies to control residual AML persisting after remission induction. Immune therapy for AML includes allogeneic stem cell transplantation, adoptive transfer of allogeneic or autologous T cells or NK cells, vaccination with leukaemia cells, dendritic cells, cell lysates, peptides and DNA vaccines and treatment with cytokines, antibodies and immunomodulatory agents. Here we describe what is known about the immunological features of AML at presentation and in remission, the current status of immunotherapy and strategies combining treatment approaches with a view to achieving leukaemia cure.
Trail‐sharing among tropical ants: interspecific use of trail pheromones?
Authors: MENZEL FLORIAN , POKORNY TAMARA , BLÜTHGEN NICO , SCHMITT THOMAS 
Published: May 2010

1. Trail‐sharing between different ant species is rare and restricted to a small number of species pairs. Its underlying mechanisms are largely unknown. For trail‐sharing to occur, two factors are required: (i) one or both species must recognise the other species or its pheromone trails and (ii) both species must tolerate each other to a certain extent to allow joint use of the trail. A species that follows another's trails can efficiently exploit the other's information on food sources contained in the pheromone trails. Hence, food competition and thus aggressive interactions between a species following another's trail and the species being followed, seem likely.2. In the present study, we investigated interspecific trail following and interspecific aggression in trail sharing associations (i) among Polyrhachis ypsilon, Camponotus saundersi, and Dolichoderus cuspidatus, and (ii) among Camponotus rufifemur and Crematogaster modiglianii. We tested whether trail‐sharing species follow each other's pheromone trails, and whether the ants tolerated or attacked their trail‐sharing partners. In both associations, we confronted workers with pheromone trails of their associated species, and, for the former association, measured interspecific aggression among the trail‐sharing species.3. In our assays, D. cuspidatus and C. rufifemur regularly followed heterospecific pheromone trails of P. ypsilon and C. modiglianii, respectively. However, only few workers of the remaining species followed heterospecific pheromone trails. Thus, shared trails of P. ypsilon and C. saundersi cannot be explained by interspecific trail‐following.4. Interspecific aggression among P. ypsilon, C. saundersi, and D. cuspidatus was strongly asymmetric, C. saundersi being submissive to the other two. All three species differentiated between heterospecific workers from the same or another site, suggesting habituation to the respective trail‐sharing partners. We therefore hypothesise that differential tolerance by dominant ant species may be mediated by selective habituation towards submissive species and this way determines the assembly of trail‐sharing associations.
Community dermatology in Debre Markos: an attempt to define children’s dermatological needs in a rural area of Ethiopia
Authors: Murgia Vitalia , Bilcha Kassahun Desalegn , Shibeshi Dagnachew 
Published: June 2010

AbstractBackground  Skin diseases are very common in rural and urban areas in developing countries. Knowledge of the real frequency of the dermatological problems of Ethiopian children could help plan future intervention for early diagnosis and low cost “good practice” therapies.Methods  We involved in the project two primary Ethiopian schools, attended by 1765 children from grade 1 to grade 4, who were screened to assess their general skin health conditions. All children were examined naked in good day light. To record data we used an EPIinfo questionnaire.Results  A total of 1104 children were screened. We registered a total number of 1086 dermatological problems, 876 of them were of infective origin mainly represented by fungal infections (36.1%). Tinea capitis represented 76% of the cases, tinea corporis 27% and tinea unguium 8%. Head lice affected 345 children. Viral infections accounted for 12%, most of them were warts.Conclusions  We think our work highlights the general health and living conditions of Ethiopian school children. The dermatological problems affecting most of the children could improve just by better skin hygiene conditions. The presence at the community level of health workers trained to perform a correct and early diagnosis and distribute efficacious, low‐cost therapies would be a relevant step forward. We think this project could help draw attention and interest to these issues.