A critical appraisal of tools available for monitoring epigenetic changes in clinical samples from patients with myeloid malignancies

Research over the past decade has confirmed that epigenetic alterations act in concert with genetic lesions to deregulate gene expression in acute myeloid leukemia and myelodysplastic syndromes. In addition, we now have the capability to pharmaceutically target epigenetic modifications, and there is an urgent need forearly validation of the efficacy of the drugs. Also, an improved understanding of the functionality of epigenetic modifications may further pave the road towards an individualized therapy. Here, we provide the pros and cons of the currently most feasible methods used for characterizing the methylome in clinical samples, and give a brief introduction to novel approaches to sequencing that may revolutionize our abilities to characterize the genomes and epigenomes in acute myeloid leukemia and myelodysplastic syndrome patients.

CoMFA and homology-based models of the glycine binding site of N-methyl-D-aspartate receptor

Homology modeling was used to build 3D models of the N-methyl-D-aspartate (NMDA) receptor glycine binding site on the basis of an X-ray structure of the water-soluble AMPA-sensitive receptor. The docking of agonists and antagonists to these models was used to reveal binding modes of ligands and to explain known structure-activity relationships. Two types of quantitative models, 3D-QSAR/CoMFA and a regression model based on docking energies, were built for antagonists (derivatives of 4-hydroxy-2-quinolone, quinoxaline-2,3-dione, and related compounds). The CoMFA steric and electrostatic maps were superimposed on the homology-based model, and a close correspondence was marked. The derived computational models have permitted the evaluation of the structural features crucial for high glycine binding site affinity and are important for the design of new ligands.

Design and experimental validation of liquid crystal-based reconfigurable reflectarray elements with improved bandwith in F-band

A reconfigurable reflectarray which exploits the dielectric anisotropy of liquid crystals (LC) has been designed to operate in the frequency range from 96 to 104 GHz. The unit cells are composed of three unequal length parallel dipoles placed above an LC substrate. The reflectarray has been designed using an accurate model which includes the effects of anisotropy and inhomogeneity. An effective permittivity that accounts for the real effects of the LC has also been used to simplify the analysis and design of the unit cells. The geometrical parameters of the cells have been adjusted to simultaneously improve the bandwidth, maximize the tunable phase-range and reduce the sensitivity to the angle of incidence. The performance of the LC based unit cells has been experimentally evaluated by measuring the reflection amplitude and phase of a reflectarray consisting of 52x54 identical cells. The good agreement between measurements and simulations validate the analysis and design techniques and demonstrate the capabilities of the proposed reflectarray to provide beam scanning in F band.

The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

Effect of interleukin-6 polymorphisms on human longevity:a systematic review and meta-analysis

Several studies have assessed changes in frequency of -174 interleukin (IL)-6 single nucleotide polymorphism (SNP) with age. If IL-6 tracks with disability and age-related diseases, then there should be reduction, in the oldest old, of the frequency of homozygous GG subjects, who produce higher IL-6 levels. However, discordant results have been obtained. To explore the relationship between this polymorphism and longevity, we analyzed individual data on long-living subjects and controls from eight case-control studies conducted in Europeans, using meta-analysis. There was no significant difference in the IL-6 genotype between the oldest old and controls (Odds Ratio [OR]=0.96; 95% C.I.: 0.77-1.20; p=0.71), but there was significant between-study heterogeneity (I2=55.5%). In a subgroup analyses when male centenarians from the three Italian studies were included, the frequency of the IL-6 -174 GG genotype was significantly lower than the other genotypes (OR=0.49; 95% C.I.: 0.31-0.80; p=0.004), with no evidence of heterogeneity (I2=0%). Our data supports a negative association between the GG genotype of IL-6 SNP and longevity in Italian centenarians, with males who carry the genotype being two times less likely to reach extreme old age compared with subjects carrying CC or CG genotypes. These findings were not replicated in other European groups suggesting a possible interaction between genetics, sex and environment in reaching longevity.

Religion and the risk of suicide: longitudinal study of over 1 million people

Background: Durkheim’s seminal historical study demonstrated that religious affiliation reduces suicide risk, but it is unclear whether this protective effect persists in modern, more secular societies.

Aims: To examine suicide risk according to Christian religious affiliation and by inference to examine underlying mechanisms for suicide risk. If church attendance is important, risk should be lowest for Roman Catholics and highest for those with no religion; if religiosity is important, then ‘conservative’ Christians should fare best.

Method: A 9-year study followed 1 106 104 people aged 16–74 years at the 2001 UK census, using Cox proportional hazards models adjusted for census-based cohort attributes.

Results: In fully adjusted models analysing 1119 cases of suicide, Roman Catholics, Protestants and those professing no religion recorded similar risks. The risk associated with conservative Christians was lower than that for Catholics (HR = 0.71, 95% CI 0.52–0.97).

Conclusions: The relationship between religious affiliation and suicide established by Durkheim may not pertain in societies where suicide rates are highest at younger ages. Risks are similar for those with and without a religious affiliation, and Catholics (who traditionally are characterised by higher levels of church attendance) do not demonstrate lower risk of suicide. However, religious affiliation is a poor measure of religiosity, except for a small group of conservative Christians, although their lower risk of suicide may be attributable to factors such as lower risk behaviour and alcohol consumption.

Mapping worlds? Excavating cartographic encounters in Plantation Ireland through GIS

This paper uses the analytical potential of Geographical Information Systems (GIS) to explore processes of map production and circulation in early-seventeenth century Ireland. The paper focuses on a group of historic maps, attributed to Josias Bodley, which were commissioned in 1609 by the English Crown to assist in the Plantation of Ulster. Through GIS and digitizing map-features, and in particular by quantifying map-distortion, it is possible to examine how these maps were made, and by whom. Statistical analyses of spatial data derived from the GIS are shown to provide a methodological basis for ‘excavating’ historical geographies of Plantation map-making. These techniques, when combined with contemporary written sources, reveal further insight on the ‘cartographic encounters’ taking place between surveyors and map-makers working in Ireland in the early 1600s, opening up the ‘mapping worlds’ which linked Ireland and Britain through the networks and embodied practices of Bodley and his map-makers.

Revised response criteria for polycythemia vera and essential thrombocythemia:an ELN and IWG-MRT consensus project

Standardized response criteria to interpret and compare clinical trials are needed for approval of new therapeutic agents by regulatory agencies. The European LeukemiaNet (ELN) response criteria for essential thrombocythemia (ET) and polycythemia vera (PV) issued in 2009 have been widely adopted as end points in a number of recent clinical trials. However, evidence exists that they do not predict response or provide clinically relevant measures of benefit for the patients. This article presents revised recommendations for assessing response in ET and PV provided by a working group established by ELN and International Working Group-Myeloproliferative Neoplasms Research and Treatment. New definitions of complete and partial remission incorporate clinical, hematological, and histological response assessments that include a standardized symptom assessment form and consider absence of disease progression and vascular events. We anticipate that these criteria will be adopted widely to facilitate the development of new and more effective therapies for ET and PV.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Adaptive calibration of a three-microphone system for acoustic waveguide characterization under time-varying conditions

The pressure and velocity field in a one-dimensional acoustic waveguide can be sensed in a non-intrusive manner using spatially distributed microphones. Experimental characterization with sensor arrangements of this type has many applications in measurement and control. This paper presents a method for measuring the acoustic variables in a duct under fluctuating propagation conditions with specific focus on in-system calibration and tracking of the system parameters of a three-microphone measurement configuration. The tractability of the non-linear optimization problem that results from taking a parametric approach is investigated alongside the influence of extraneous measurement noise on the parameter estimates. The validity and accuracy of the method are experimentally assessed in terms of the ability of the calibrated system to separate the propagating waves under controlled conditions. The tracking performance is tested through measurements with a time-varying mean flow, including an experiment conducted under propagation conditions similar to those in a wind instrument during playing.

Flexural behaviour of external R/C steel fibre reinforced beam-column joints

A softened strut-and-tie macro model able to reproduce the flexural behaviour of
external beam-column joint is presented. The model is specific for concrete with hooked steel fibres (FRC) and it is designed to calculate the flexural response, as load-deflection curve, of a beam-column sub-assemblages. The model considers the presence of a constant vertical load acting on the column and of a monotonically increasing lateral force applied at the tip of the beam.

Comportamento flessionale di nodi esterni in calcestruzzo fibrorinforzato

SOMMARIO – Si presenta un macro modello di tipo reticolare in grado di riprodurre il comportamento in presenza di taglio e momento di nodi esterni trave-colonna di telai in calcestruzzo fibrorinforzato con fibre di acciaio
uncinato ed ordinario. Il caricamento del sistema è di tipo monotono come nel caso dell’analisi di pushover. Il modello considera la presenza di armature orizzontali e verticali della regione nodale e tiene in conto delle modalità
di rottura legate allo snervamento delle barre e allo schiacciamento delle regioni compresse in regime di sforzi pluriassiali. Il modello include le deformazioni flessionali della trave e della colonna in presenza di sforzo normale costante e restituisce la risposta del sistema colonna-nodo-trave (sub-assembralggio) tramite le curve carico-freccia all’estremità della semitrave. Per i singoli costituenti (trave, colonna e nodo) si è considerata la prima fessurazione, lo snervamento e lo schiacciamento delle regioni compresse e si sono fornite precise indicazioni sulla sequenza degli eventi che come è noto sono di fondamentale importanza per lo sviluppo di un progetto plastico che rispetti la gerarchia delle resistenze. Con l’uso del modello il controllo della gerarchia delle resistenze avviene a livello sezionale (lo snervamento delle barre deve avvenire prima dello schiacciamento delle regioni compresse) o di macro elemento (nella regione nodale lo snervamento delle staffe precede la crisi dei puntoni) e dell’intero elemento
sub-assemblaggio trave debole, colonna forte e nodo sovraresistente.
La risposta ottenuta con i modello proposto è in buon accordo con le risposte sperimentali disponibili in letteratura (almeno in termini di resistenza del sub-assemblaggio). Il modello è stato ulteriormente validato con analisi
numeriche agli elementi finiti condotte con il codice ATENA-2D. Le analisi numeriche sono state condotte utilizzando per il calcestruzzo fibroso adeguate leggi costitutive proposte dagli autori ed in grado di cogliere gli effetti
di softening e di resistenza residua a trazione legati alla presenza di fibre. Ulteriori sviluppi del modello saranno indirizzati a includere gli effetti di sfilamento delle barre d’armatura della trave e del conseguente degrado delle
tensioni d’aderenza per effetto di carichi monotonici e ciclici.

SUMMARY – A softened strut-and-tie macro model able to reproduce the flexural behavior of external beam-tocolumn joints with the presence of horizontal and vertical steel bars, including softening of compressed struts and yielding of main and secondary steel bars, is presented, to be used for the pushover analysis. The model proposed is able to calculate also the flexural response of fibrous reinforced concrete (FRC) beam-to-column sub-assemblages in term of a multilinear load-deflection curves. The model is able to take into account of the tensile behavior of main bars embedded in the surrounding concrete and of the softening of the compressed strut, the arrangement and percentage of the steel bars, the percentage and the geometry of steel fibers. First cracking, yielding of main steel and crushing of concrete were identified to determine the corresponding loads and displacement and to plot the simplified monotonic load-deflection curves of the sub-assemblages subjected in the column to constant vertical
load and at the tip of the beam to monotonically increasing lateral force. Through these load-delfection curves the component (beam, joint and column) that first collapse can be recognized and the capacity design can be verified.
The experimental results available in the literature are compared with the results obtained through the proposed model. Further, a validation of the proposed model is numerically made by using a non linear finite element program (ATENA-2D) able to analyze the flexural behavior of sub-assemblages.