bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haploview: Visualization and Analysis of SNP Genotype Data
Authors: Barrett Jeffrey C. 
Published: October 2009

INTRODUCTIONAssociation studies involve accessing, parsing, generating, and analyzing large volumes of data, often carried out in many steps over many months. Large-scale surveys of genetic variation, such as the International HapMap Project, and rapidly increasing volumes of single-nucleotide polymorphism (SNP) genotyping data have created exciting opportunities for association studies. However, they have further exacerbated the difficulty of curating and analyzing such data. Haploview is a program developed in Mark Daly’s lab at the Broad Institute of MIT and Harvard, which is designed to bundle many everyday analysis tasks into one easy-to-use package. Haploview has several features that are useful throughout different phases of association studies. Several of these features are illustrated in this article by following a hypothetical association study from design to execution. Haploview is used to (1) analyze HapMap data and choose tag-SNPs, (2) evaluate the quality of disease genotype data, (3) test for association, and (4) evaluate a region for follow-up of a positive association.
High-Resolution Dual-Trap Optical Tweezers with Differential Detection: Data Collection and Instrument Calibration: Figure 1.
Authors: Bustamante Carlos , Chemla Yann R. , Moffitt Jeffrey R. 
Published: October 2009

INTRODUCTIONOptical traps or “optical tweezers” have become an indispensable tool in understanding fundamental biological processes. Dual-trap optical tweezers with differential detection have the advantage that the instrument is decoupled from sources of environmental noise, thereby minimizing interference of signal and maximizing stability and spatial resolution. In this article, we describe methods of data detection and calibration for our dual-trap design.
High-Resolution Dual-Trap Optical Tweezers with Differential Detection: Minimizing the Influence of Measurement Noise
Authors: Bustamante Carlos , Chemla Yann R. , Moffitt Jeffrey R. 
Published: October 2009

INTRODUCTIONOptical traps or “optical tweezers” have become an indispensable tool in understanding fundamental biological processes. The environment, the instrument components, and the overall design all have important roles in determining the spatial resolution of an optical trap. However, even with careful attention to these details, the spatial resolution of the optical tweezers is still fundamentally limited by the forces that induce Brownian fluctuations of the trapped microspheres. In this article, we focus on the ways in which the design and implementation of an experiment--the choice of bead size, tether length, and even the method in which the motions of the beads are monitored--can have a large impact on the fundamental resolution of the measurement. By investigating how the Brownian fluctuations depend on experimental parameters and the detection method, we develop a set of guidelines for designing a high-resolution experiment, with a prescription for minimizing the effect of Brownian fluctuations, thus maximizing the resolution of the experiment.
High-Resolution Dual-Trap Optical Tweezers with Differential Detection: Alignment of Instrument Components: Figure 1.
Authors: Bustamante Carlos , Chemla Yann R. , Moffitt Jeffrey R. 
Published: October 2009

INTRODUCTIONOptical traps or “optical tweezers” have become an indispensable tool in understanding fundamental biological processes. Using our design, a dual-trap optical tweezers with differential detection, we can detect length changes to a DNA molecule tethering the trapped beads of 1 bp. By forming two traps from the same laser and maximizing the common optical paths of the two trapping beams, we decouple the instrument from many sources of environmental and instrumental noise that typically limit spatial resolution. The performance of a high-resolution instrument--the formation of strong traps, the minimization of background signals from trap movements, or the mitigation of the axial coupling, for example--can be greatly improved through careful alignment. This procedure, which is described in this article, starts from the laser and advances through the instrument, component by component. Alignment is complicated by the fact that the trapping light is in the near infrared (NIR) spectrum. Standard infrared viewing cards are commonly used to locate the beam, but unfortunately, bleach quickly. As an alternative, we use an IR-viewing charge-coupled device (CCD) camera equipped with a C-mount telephoto lens and display its image on a monitor. By visualizing the scattered light on a pair of irises of identical height separated by >12 in., the beam direction can be set very accurately along a fixed axis.
Extraction of RNA from the Plant Kalanchoë daigremontiana
Authors: Garcês Helena , Sinha Neelima 
Published: October 2009

INTRODUCTIONThis protocol describes how to isolate total RNA from several tissues of Kalanchoë daigremontiana. Total RNA can be isolated by using the TRI-reagent method, scaled up for processing 2 g of tissue, or by using the protocol described here, which gives higher concentrations of high quality RNA. The resulting RNA can be used for various applications including generation of cDNA for reverse transcriptase-PCR (RT-PCR), Northern blots, or other purposes.
Refined candidate region specified by haplotype sharing for Escherichia coli F4ab/F4ac susceptibility alleles in pigs
Authors: Jacobsen M. , Kracht S. S. , Esteso G. , Cirera S. , Edfors I. , Archibald A. L. , Bendixen C. , Andersson L. , Fredholm M. , Jørgensen C. B. 
Published: October 2009

SummaryInfection of the small intestine by enterotoxigenic Escherichia coli F4ab/ac is a major welfare problem and financial burden for the pig industry. Natural resistance to this infection is inherited as a Mendelian recessive trait, and a polymorphism in the MUC4 gene segregating for susceptibility/resistance is presently used in a selection programme by the Danish pig breeding industry. To elucidate the genetic background involved in E. coli F4ab/ac susceptibility in pigs, a detailed haplotype map of the porcine candidate region was established. This region covers approximately 3.7 Mb. The material used for the study is a three generation family, where the founders are two Wild boars and eight Large White sows. All pigs have been phenotyped for susceptibility to F4ab/ac using an adhesion assay. Their haplotypes are known from segregation analysis using flanking markers. By a targeted approach, the candidate region was subjected to screening for polymorphisms, mainly focusing on intronic sequences. A total of 18 genes were partially sequenced, and polymorphisms were identified in GP5, CENTB2, APOD, PCYT1A, OSTalpha, ZDHHC19, TFRC, ACK1, MUC4, MUC20, KIAA0226, LRCH3 and MUC13. Overall, 227 polymorphisms were discovered in the founder generation. The analysis revealed a large haplotype block, spanning at least 1.5 Mb around MUC4, to be associated with F4ab/ac susceptibility.
The phenotypic and functional characteristics of umbilical cord blood and peripheral blood natural killer cells
Authors: Verneris Michael R. , Miller Jeffrey S. 
Published: October 2009

SummaryAllogeneic hematopoietic cell transplantation can be curative for patients with high‐risk acute leukaemia. Umbilical cord blood (UCB) is an increasingly used source of allogeneic stem cells for patients who are in need of a transplant, but do not have a sibling donor. This review highlights the similarities and differences between the natural killer (NK) cells obtained from adult peripheral blood (PB) and UCB. These two cell sources show similar percentages of NK cells, including the major CD56dim and CD56bright subpopulations. UCB also contains an additional CD56−CD16+ subset, not typically found in PB. In addition, there are a number of progenitor cell populations in UCB that can give rise to NK cells. Some studies showed that UCB NK cells express a relatively higher percentage of inhibitory receptors (CD94/NKG2A and killer‐cell immunoglobulin‐like receptors) and less adhesion molecules. Resting UCB NK cells also show significantly less cytotoxicity compared to PB NK cells. However, following cytokine stimulation, the cytotoxicity of UCB NK cells can be rapidly increased to levels that are comparable to PB NK cells. Activation and expansion protocols for UCB NK cells are briefly reviewed. Lastly, we outline the early use of UCB NK cells in clinical trials.
Improving cord blood transplantation in children
Authors: Locatelli Franco 
Published: October 2009

SummaryUmbilical cord blood transplantation (UCBT) is widely used to treat children affected by many disorders. In comparison to bone marrow transplantation, the advantages of UCBT are represented by lower incidence and severity of graft‐versus‐host disease, easier procurement and prompter availability of cord blood cells, and by the possibility of using donors showing human leucocyte antigen disparities with the recipient. Despite these advantages, the large experience gained over the last decade has clearly demonstrated that UCBT patients may be exposed to an increased risk of early fatal complications, due to the lower engraftment rate of donor haematopoiesis, delayed kinetics of neutrophil recovery and lack of adoptive transfer of pathogen‐specific memory T‐cells. An inverse correlation between the number of nucleated cord blood cells infused per kilogramme recipient body weight and the risk of dying from transplantation‐related causes exists. Thus, it is not surprising that strategies aimed at increasing the number of cord blood progenitors, favouring stem cell homing, and transferring pathogen‐specific lymphocytes, have been recently investigated. In particular, selection of the richest cord blood units, infusion of 2 units in the same recipient, intrabone injection of cord blood cells, and transplantation of ex‐vivo expanded progenitors can contribute to improve the results of UCBT.
Linking reductionist science and holistic policy using systematic reviews: unpacking environmental policy questions to construct an evidence‐based framework
Authors: Pullin Andrew S. , Knight Teri M. , Watkinson Andrew R. 
Published: October 2009

Summary 1. There is a mismatch between broad holistic questions typically posed in policy formation and narrow reductionist questions that are susceptible to scientific method. This inhibits the two‐way flow of information at the science‐policy interface and weakens the impact of applied ecology on environmental policy. 2. We investigate the approaches to building policy in the health services as a model to help establish a framework in applied ecology and environmental management by which reductionist science can underpin decision making at the policy level. 3. A comparison of policy documents in the health and environmental sectors reveals many similarities in identifying approaches and specific interventions that might achieve policy objectives. The difference is that in the health services, information on the effectiveness of potential interventions is far more readily available through the collaborative process of systematic review. 4.
Synthesis and applications. Decision makers are increasingly looking to produce policies that are shaped by evidence through evidence‐based policy making. The approach that we outline here provides a framework for structuring systematic reviews to deliver the evidence on key policy issues in a way that will see a faster return and provide better use of the systematic review methodology in environmental management.
Marked elevation of serum macrophage migration inhibitory factor levels in patients with pemphigus vulgaris
Authors: Namazi Mohammad Reza , Fallahzadeh Mohammad Kazem , Shaghelani Hassan , Kamali‐Sarvestani Eskandar 
Published: October 2009

AbstractBackground  There is ample evidence for involvement of macrophage migration inhibitory factor (MIF) in autoimmune and inflammatory diseases.Objective  The aim of this study was to determine whether MIF levels were raised in the sera of patients with pemphigus vulgaris (PV).Methods  Serum MIF levels were measured using ELISA method in 22 patients with active PV and 21 age‐ and sex‐matched healthy controls and the results were compared with each other.Results  The mean serum MIF levels was significantly higher in PV patients than in control subjects (11.99 ± 1.63 pg/m vs. 1.83 ± 0.22 pg/ml; P‐value = 0.0001).Conclusions  Elevated MIF levels in the sera of PV patients could participate in disease induction by activation of T cells as well as induction of autoantibody production by B cells. Given that MIF counter‐regulates the effects of steroids, MIF antagonists may prove to be very effective, novel steroid‐sparing agents for this life‐threatening conundrum.
A network analysis of the single nucleotide polymorphisms in acute allergic diseases
Authors: Renkonen J. , Mattila P. , Parviainen V. , Joenväärä S. , Toppila‐Salmi S. , Renkonen R. 
Published: October 2009

AbstractBackground:  Genetics of acute allergies has focused on identifying single nucleotide polymorphisms (SNPs) within genes relevant in the pathogenesis. In this study, we begin a systems biology analysis of the interconnectivity and biological functions of these genes, their transcripts and their corresponding proteins.Methods:  The literature (Pubmed) was searched for SNPs within genes relevant in acute allergic diseases. The SNP‐modified genes were converted to corresponding proteins and their protein–protein interactions were searched from six different databases. This interaction network was analysed with annotated vocabularies (ontologies), such as Gene Ontology, Reactome and Nature pathway interaction database. Time‐series transcriptomics was performed with nasal epithelial cells obtained from allergic patients and their healthy control subjects.Results:  A total of 39 genes with SNPs related to acute allergic diseases were found from a literature search. The corresponding proteins were then hooked into a large protein–protein interaction network with the help of various databases. Twenty‐five SNP‐related proteins had more than one interacting protein and a network contained 95 proteins, and 182 connections could be generated. This network was 10‐fold enriched with protein kinases and proteins involved in the host–virus interaction compared with background human proteome. Finally, eight of the 95 nodes on our network displayed nasal epithelial transcriptomal regulation in a time‐series analysis collected from birch allergic patients during the spring pollen season.Conclusions:  Signal transduction with special reference to host–virus interactions dominated in the allergy‐related protein interaction network. Systems level analysis of allergy‐related mutation can provide new insights into pathogenetic mechanisms of the diseases.
Characterization and comparison of commercially available mite extracts for in vivo diagnosis
Authors: Brunetto B. , Tinghino R. , Braschi M. C. , Antonicelli L. , Pini C. , Iacovacci P. 
Published: October 2009

To cite this article: Brunetto B, Tinghino R, Braschi MC, Antonicelli L, Pini C, Iacovacci P. Characterization and comparison of commercially available mite extracts for in vivo diagnosis. Allergy 2010; 65: 184–190.AbstractBackground:  Assessment of sensitization by allergen‐specific IgE testing and skin prick testing (SPT) are primary tools in routine clinical diagnosis of allergies. To perform a correct diagnosis, it is critical that the allergen reagent used contains an adequate amount of all relevant components. This study aimed at evaluating commercially available mite extracts for in vivo diagnosis from eight manufacturers.Methods:  Eight extracts from Dermatophagoides pteronyssinus and eight from Dermatophagoides farinae were analysed for total protein content by Bradford and for major allergen content by ELISA. SDS‐PAGE, immunoblotting and SPT were also carried out.Results:  The protein amount ranged from 27.7 μg/ml extract to 361.1 μg/ml (D. pteronyssinus) and from 20.3 to 353.0 μg/ml (D. farinae). In regards major allergen concentration, Der p 1 ranged from 9.6 to 36.2 μg/ml, Der f 1 26.5–196.1 μg/ml, mite group 2 0.7–31.7 μg/ml in D. pteronyssinus and 1.3–10.4 μg/ml in D. farinae. SDS‐PAGE experiments showed that some components are poorly represented or absent in extracts from most manufacturers. Similar results were obtained by IgE‐immunoblotting and SPT with 10 mite allergic patients confirmed a broad spectrum of reactivity of the extracts in the same subject.Conclusions:  Immunochemical analysis showed a heterogeneous amount of component/s among mite extracts from different manufacturers. These data were confirmed by in vivo testing, suggesting that, for some of the patient tested, the absence of relevant allergens could strongly affect the diagnosis.
Inhaled vs subcutaneous effects of a dual IL‐4/IL‐13 antagonist in a monkey model of asthma
Authors: Tomkinson A. , Tepper J. , Morton M. , Bowden A. , Stevens L. , Harris P. , Lindell D. , Fitch N. , Gundel R. , Getz E. B. 
Published: October 2009

AbstractBackground:  Pitrakinra is a recombinant protein derived from human interleukin‐4 (IL‐4) that binds to IL‐4Rα and acts as a competitive antagonist of IL‐4 and IL‐13. The studies reported here compare the dose‐ranging effects of pitrakinra on allergen‐induced airway hyperresponsiveness (AHR) and airway eosinophilia when administered subcutaneously (s.c.) or by inhalation to the Ascaris suum‐sensitive cynomolgus monkey for the purpose of elucidating the primary site of pitrakinra’s anti‐asthmatic action.Methods:  Airway responsiveness to inhaled methacholine and bronchoalveolar lavage cell composition was determined before and after three allergen exposures with a 1‐week course of twice‐daily (b.i.d.) s.c. or inhaled pitrakinra or placebo treatment.Results:  Treatment with s.c. pitrakinra significantly reduced allergen‐induced AHR, with a maximum effect of a 2.8‐ to 3.8‐fold increase in methacholine PC100 relative to control (P < 0.05) observed at b.i.d. s.c. doses of 0.05–0.5 mg/kg. Inhaled pitrakinra also significantly reduced AHR with a similar maximum effect of a 2.8‐ to 3.2‐fold increase in methacholine PC100 relative to control (P < 0.05) at nominal b.i.d. doses of 3–100 mg. The maximal effect on AHR following inhalation was observed at a plasma concentration which exhibited no efficacy via the subcutaneous route. The effect of pitrakinra on lung eosinophilia was not statistically significant following either route of administration, although lung eosinophil count was reduced in all studies relative to control.Conclusion:  Local administration of pitrakinra to the lung is sufficient to inhibit AHR, one of the cardinal features of asthma, indicating the therapeutic potential of inhaled pitrakinra in the treatment of atopic asthma.
Polymorphisms in IL13 pathway genes in asthma and chronic obstructive pulmonary disease
Authors: Beghé B. , Hall I. P. , Parker S. G. , Moffatt M. F. , Wardlaw A. , Connolly M. J. , Fabbri L. M. , Ruse C. , Sayers I. 
Published: October 2009

To cite this article: Beghé B, Hall IP, Parker SG, Moffatt MF, Wardlaw A, Connolly MJ, Fabbri LM, Ruse C, Sayers I. Polymorphisms in IL13 pathway genes in asthma and chronic obstructive pulmonary disease. Allergy 2010; 65: 474–481.AbstractBackground:  Asthma and chronic obstructive pulmonary disease (COPD) are chronic respiratory diseases involving an interaction between genetic and environmental factors. Interleukin‐13 (IL13) has been suggested to have a role in both asthma and COPD. We investigated whether single nucleotide polymorphisms (SNPs) in the IL13 pathway may contribute to the susceptibility and severity of asthma and COPD in adults.Methods:  Twelve SNPs in IL13 pathway genes –IL4, IL13, IL4RA, IL13RA1, IL13RA2 and STAT6– were genotyped in subjects with asthma (n = 299) and in subjects with COPD or healthy smokers (n = 992). Genetic association was evaluated using genotype and allele models for asthma severity, atopy phenotypes and COPD susceptibility. Linear regression was used to determine the effects of polymorphism on baseline lung function (FEV1, FEV1/FVC).Results:  In asthmatics, three IL13 SNPs – rs1881457(–1512), rs1800925(–1111) and rs20541(R130Q) – were associated with atopy risk. One SNP in IL4RA1 [rs1805010(I75V)] was associated with asthma severity, and several IL13 SNPs showed borderline significance. IL13 SNPs rs1881457(–1512) and rs1800925(–1111) were associated with better FEV1 and FEV1/FVC in asthmatics. IL13 SNPs rs2066960(intron 1), rs20541(R130Q) and rs1295685(exon 4) were associated with COPD risk and lower baseline lung function in the recessive model. In females, but not in males, rs2250747 of the IL13RA1 gene was associated with COPD and lower FEV1.Conclusion:  These data suggest that IL13 SNPs (promoter and coding region) and, to a lesser extent, IL4RA SNPs may contribute to atopy and asthma. We also provide tentative evidence that IL13 SNPs in the coding region may be of significance in COPD susceptibility.
Silent mysteries: epigenetic paradigms could hold the key to conquering the epidemic of allergy and immune disease
Authors: Martino D. J. , Prescott S. L. 
Published: October 2009

AbstractEpigenetic mechanisms provide new insights into how environmental changes may mediate the increasing propensity for complex immune diseases such as allergic disease. There is now strong evidence that early environmental exposures play a key role in activating or silencing genes by altering DNA and histone methylation, histone acetylation and chromatin structure. These modifications determine the degree of DNA compaction and accessibility for gene transcription, altering gene expression, phenotype and disease susceptibility. While there is already evidence that a number of early environmental exposures are associated with an increased risk of allergic disease, several new studies indicate in utero microbial and dietary exposures can modify gene expression and allergic disease propensity through epigenetic modification. This review explores the evidence that immune development is under clear epigenetic regulation, including the pattern of T helper (Th)1 and Th2 cell differentiation, regulatory T cell differentiation, and more recently, Th17 development. It also considers the mechanisms of epigenetic regulation and early immune defects in allergy prone neonates. The inherent plasticity conferred by epigenetic mechanisms clearly also provides opportunities for environmental strategies that can re‐programme gene expression for disease prevention. Identifying genes that are differentially silenced or activated in relation to subsequent disease will not only assist in identifying causal pathways, but may also help identify the contributing environmental factors.