Adaptation of the methotrexate in rheumatoid arthritis knowledge questionnaire (MiRAK) for use with parents of children with juvenile idiopathic arthritis (JIA)

Background: Although Methotrexate (MTX) is one of the most commonly prescribed disease-modifying drugs in JIA no questionnaire exists that assesses the knowledge of parents about this drug. A 60-item questionnaire was recently developed to measure rheumatoid arthritis (RA) patients’ knowledge about MTX; the Methotrexate in Rheumatoid Arthritis Knowledge Test (MiRAK; Ciciriello et al. (Arthritis Rheum 62:10–1009, 2010)). This study aimed to adapt the MiRAK for parents of children with JIA. Methods: Adaption of the MiRAK involved: 1) email consultations with clinicians working in the field of paediatric rheumatology (Panel 1) to ascertain the potential adaptations of the MiRAK from a clinical perspective, 2) synthesis of clinicians’ suggestions by a panel of experts, researchers and MiRAK developers (Panel 2) to reach consensus on which items needed to be modified and create a draft Methotrexate in Juvenile Idiopathic Arthritis Knowledge Test (MiJIAK), 3) a review of the draft by 5 parents of children with JIA (Panel 3) using the cognitive ‘think-aloud’ method, 4) a second consultation with Panel 2 to review parents’ suggestions and determine the final items. Results: A total of 9 items remained unchanged, e.g. “Methotrexate is effective at relieving joint stiffness”, 19 were deemed inappropriate in the paediatric setting and deleted, e.g. “It is safe to become pregnant 3 weeks after methotrexate has been stopped”, 32 underwent editorial changes largely to indicate that the questionnaire was about the children with JIA, e.g. “If you forget to give a dose of Methotrexate, you can still take it the next day” became “If your child misses a dose of Methotrexate, they can still take it the next day”, and 1 new item was added. A new 42-item questionnaire was produced and was found to be well understood by parents of children with JIA. Conclusions: The systematic modification of the MiRAK, a patient-centred MTX knowledge questionnaire, has generated a comprehensive new questionnaire for use in the JIA setting. The wide consultation process, including cognitive testing, has ensured the tool is both relevant and acceptable to clinicians and will therefore be a valuable addition in understanding the parents’ perspective of this treatment in JIA

A phase I pharmacokinetic and pharmacodynamic study of the oral mitogen-activated protein kinase kinase (MEK) inhibitor, WX-554, in patients with advanced solid tumours

Purpose: We performed a multi-centre phase I study to assess the safety, pharmacokinetics (PK) and pharmacodynamics (PD) of the orally available small molecule mitogen-activated protein kinase kinase (MEK) 1/2 inhibitor, WX-554, and to determine the optimal biological dose for subsequent trials. Experimental design: Patients with treatment-refractory, advanced solid tumours, with adequate performance status and organ function were recruited to a dose-escalation study in a standard 3 + 3 design. The starting dose was 25 mg orally once weekly with toxicity, PK and PD guided dose-escalation with potential to explore alternative schedules. Results: Forty-one patients with advanced solid tumours refractory to standard therapies and with adequate organ function were recruited in eight cohorts up to doses of 150 mg once weekly and 75 mg twice weekly. No dose-limiting toxicities were observed during the study, and a maximum tolerated dose (MTD) was not established. The highest dose cohorts demonstrated sustained inhibition of extracellular signal-regulated kinase (ERK) phosphorylation in peripheral blood mononuclear cells following ex-vivo phorbol 12-myristate 13-acetate stimulation. There was a decrease of 70 ± 26% in mean phosphorylated (p)ERK in C1 day 8 tumour biopsies when compared with pre-treatment tumour levels in the 75 mg twice a week cohort. Prolonged stable disease (>6 months) was seen in two patients, one with cervical cancer and one with ampullary carcinoma. Conclusions: WX-554 was well tolerated, and an optimal biological dose was established for further investigation in either a once or twice weekly regimens. The recommended phase 2 dose is 75 mg twice weekly

Adaptation of the methotrexate in rheumatoid arthritis knowledge questionnaire (MiRAK) for use with parents of children with juvenile idiopathic arthritis: a qualitative study

BACKGROUND: Although Methotrexate (MTX) is one of the most commonly prescribed disease-modifying drugs in JIA no questionnaire exists that assesses the knowledge of parents about this drug. A 60-item questionnaire was recently developed to measure rheumatoid arthritis (RA) patients\u27 knowledge about MTX; the Methotrexate in Rheumatoid Arthritis Knowledge Test (MiRAK; Ciciriello et al. (Arthritis Rheum 62:10-1009, 2010)). This study aimed to adapt the MiRAK for parents of children with JIA. METHODS: Adaption of the MiRAK involved: 1) email consultations with clinicians working in the field of paediatric rheumatology (Panel 1) to ascertain the potential adaptations of the MiRAK from a clinical perspective, 2) synthesis of clinicians\u27 suggestions by a panel of experts, researchers and MiRAK developers (Panel 2) to reach consensus on which items needed to be modified and create a draft Methotrexate in Juvenile Idiopathic Arthritis Knowledge Test (MiJIAK), 3) a review of the draft by 5 parents of children with JIA (Panel 3) using the cognitive \u27think-aloud\u27 method, 4) a second consultation with Panel 2 to review parents\u27 suggestions and determine the final items. RESULTS: A total of 9 items remained unchanged, e.g. "Methotrexate is effective at relieving joint stiffness", 19 were deemed inappropriate in the paediatric setting and deleted, e.g. "It is safe to become pregnant 3 weeks after methotrexate has been stopped", 32 underwent editorial changes largely to indicate that the questionnaire was about the children with JIA, e.g. "If you forget to give a dose of Methotrexate, you can still take it the next day" became "If your child misses a dose of Methotrexate, they can still take it the next day", and 1 new item was added. A new 42-item questionnaire was produced and was found to be well understood by parents of children with JIA. CONCLUSIONS: The systematic modification of the MiRAK, a patient-centred MTX knowledge questionnaire, has generated a comprehensive new questionnaire for use in the JIA setting. The wide consultation process, including cognitive testing, has ensured the tool is both relevant and acceptable to clinicians and will therefore be a valuable addition in understanding the parents\u27 perspective of this treatment in JIA

Caterpillars on a Phytochemical Landscape: The Case of Alfalfa and the Melissa Blue Butterfly

Modern metabolomic approaches that generate more comprehensive phytochemical profiles than were previously available are providing new opportunities for understanding plant‐animal interactions. Specifically, we can characterize the phytochemical landscape by asking how a larger number of individual compounds affect herbivores and how compounds covary among plants. Here we use the recent colonization of alfalfa (Medicago sativa) by the Melissa blue butterfly (Lycaeides melissa) to investigate the effects of indivdiual compounds and suites of covarying phytochemicals on caterpillar performance. We find that survival, development time, and adult weight are all associated with variation in nutrition and toxicity, including biomolecules associated with plant cell function as well as putative anti‐herbivore action. The plant‐insect interface is complex, with clusters of covarying compounds in many cases encompassing divergent effects on different aspects of caterpillar performance. Individual compounds with the strongest associations are largely specialized metabolites, including alkaloids, phenolic glycosides, and saponins. The saponins are represented in our data by more than 25 individual compounds with beneficial and detrimental effects on L. melissa caterpillars, which highlights the value of metabolomic data as opposed to approaches that rely on total concentrations within broad defensive classes

The high-precision, charge-dependent Bonn nucleon-nucleon potential (CD-Bonn)

We present a charge-dependent nucleon-nucleon (NN) potential that fits the world proton-proton data below 350 MeV available in the year of 2000 with a chi^2 per datum of 1.01 for 2932 data and the corresponding neutron-proton data with chi^2/datum = 1.02 for 3058 data. This reproduction of the NN data is more accurate than by any phase-shift analysis and any other NN potential. The charge-dependence of the present potential (that has been dubbed `CD-Bonn') is based upon the predictions by the Bonn Full Model for charge-symmetry and charge-independence breaking in all partial waves with J <= 4. The potential is represented in terms of the covariant Feynman amplitudes for one-boson exchange which are nonlocal. Therefore, the off-shell behavior of the CD-Bonn potential differs in a characteristic and well-founded way from commonly used local potentials and leads to larger binding energies in nuclear few- and many-body systems, where underbinding is a persistent problem.Comment: 69 pages (RevTex) including 20 tables and 9 figures (ps files

Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species

Studies of reproductive isolation between homoploid hybrid species and their parent species have rarely been carried out. Here we investigate reproductive barriers between a recently recognized hybrid bird species, the Italian sparrow Passer italiae and its parent species, the house sparrow P. domesticus and Spanish sparrow P. hispaniolensis. Reproductive barriers can be difficult to study in hybrid species due to lack of geographical contact between taxa. However, the Italian sparrow lives parapatrically with the house sparrow and both sympatrically and parapatrically with the Spanish sparrow. Through whole-transcriptome sequencing of six individuals of each of the two parent species we identified a set of putatively parent species-diagnostic single nucleotide polymorphism (SNP) markers. After filtering for coverage, genotyping success (>97%) and multiple SNPs per gene, we retained 86 species-informative, genic, nuclear and mitochondrial SNP markers from 84 genes for analysis of 612 male individuals. We show that a disproportionately large number of sex-linked genes, as well as the mitochondria and nuclear genes with mitochondrial function, exhibit sharp clines at the boundaries between the hybrid and the parent species, suggesting a role for mito-nuclear and sex-linked incompatibilities in forming reproductive barriers. We suggest that genomic conflict via interactions between mitochondria and sex-linked genes with mitochondrial function ("mother's curse") at one boundary and centromeric drive at the other may best explain our findings. Hybrid speciation in the Italian sparrow may therefore be influenced by mechanisms similar to those involved in non-hybrid speciation, but with the formation of two geographically separated species boundaries instead of one. Spanish sparrow alleles at some loci have spread north to form reproductive barriers with house sparrows, while house sparrow alleles at different loci, including some on the same chromosome, have spread in the opposite direction to form barriers against Spanish sparrows

System for deployment of groups of unmanned micro aerial vehicles in GPS-denied environments using onboard visual relative localization

A complex system for control of swarms of micro aerial vehicles (MAV), in literature also called as unmanned aerial vehicles (UAV) or unmanned aerial systems (UAS), stabilized via an onboard visual relative localization is described in this paper. The main purpose of this work is to verify the possibility of self-stabilization of multi-MAV groups without an external global positioning system. This approach enables the deployment of MAV swarms outside laboratory conditions, and it may be considered an enabling technique for utilizing fleets of MAVs in real-world scenarios. The proposed visual-based stabilization approach has been designed for numerous different multi-UAV robotic applications (leader-follower UAV formation stabilization, UAV swarm stabilization and deployment in surveillance scenarios, cooperative UAV sensory measurement) in this paper. Deployment of the system in real-world scenarios truthfully verifies its operational constraints, given by limited onboard sensing suites and processing capabilities. The performance of the presented approach (MAV control, motion planning, MAV stabilization, and trajectory planning) in multi-MAV applications has been validated by experimental results in indoor as well as in challenging outdoor environments (e.g., in windy conditions and in a former pit mine)

Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm

Background Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is also true for structural variation detected from sequence data. However, the genotypes at known variable sites can only be inferred with uncertainty from low coverage data. Thus, statistical approaches that infer genotype likelihoods, test hypotheses, and estimate population parameters without requiring accurate genotypes are becoming popular. Unfortunately, the current implementations of these methods are intended to analyse only single nucleotide and short indel variation, and they usually assume that the two alleles in a heterozygous individual are sampled with equal probability. This is generally false for structural variants detected with paired ends or split reads. Therefore, the population genetics of structural variants cannot be studied, unless a painstaking and potentially biased genotyping is performed first. Results We present svgem, an expectation-maximization implementation to estimate allele and genotype frequencies, calculate genotype posterior probabilities, and test for Hardy-Weinberg equilibrium and for population differences, from the numbers of times the alleles are observed in each individual. Although applicable to single nucleotide variation, it aims at bi-allelic structural variation of any type, observed by either split reads or paired ends, with arbitrarily high allele sampling bias. We test svgem with simulated and real data from the 1000 Genomes Project. Conclusions svgem makes it possible to use low-coverage sequencing data to study the population distribution of structural variants without having to know their genotypes. Furthermore, this advance allows the combined analysis of structural and nucleotide variation within the same genotype-free statistical framework, thus preventing biases introduced by genotype imputation

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

<p>Abstract</p> <p>Background</p> <p>Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as <it>reticulate evolutionary events</it>, result in <it>networks</it>, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.</p> <p>Results</p> <p>In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or <it>evolutionary networks</it>, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks – trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees.</p> <p>Conclusion</p> <p>The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed eNewick format for compact representation of evolutionary networks, a feature that allows for efficient interoperability of evolutionary network software tools. Currently, all utilities in PhyloNet are invoked on the command line.</p