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.

Chiton phylogeny (Mollusca Polyplacophora) and the placement of the enigmatic species Choriplax grayi (H. Adams & Angas)

Shallow marine chitons (Mollusca:Polyplacophora:Chitonida) are widespread and well described from established morphoanatomical characters, yet key aspects of polyplacophoran phylogeny have remained unresolved. Several species, including Hemiarthrum setulosum Carpenter in Dall, 1876, and especially the rare and enigmatic Choriplax grayi (Adams & Angas, 1864), defy systematic placement. Choriplax is known from only a handful of specimens and its morphology is a mosaic of key taxonomic features from two different clades. Here, new molecular evidence provides robust support for its correct association with a third different clade: Choriplax is placed in the superfamily Mopalioidea. Hemiarthrum is included in Cryptoplacoidea, as predicted from morphological evidence. Our multigene analysis of standard nuclear and mitochondrial markers demonstrates that the topology of the order Chitonida is divided into four clades, which have also been recovered in previous studies: Mopalioidea is sister to Cryptoplacoidea, forming a clade Acanthochitonina. The family Callochitonidae is sister to Acanthochitonina. Chitonoidea is resolved as the earliest diverging group within Chitonida. Consideration of this unexpected result for Choriplax and our well-supported phylogeny has revealed differing patterns of shell reduction separating the two superfamilies within Acanthochitonina. As in many molluscs, shell reduction as well as the de novo development of key shell features has occurred using different mechanisms, in multiple lineages of chitons.

A spectroscopically normal type Ic supernova from a very massive progenitor

We present observations of the Type Ic supernova (SN Ic) 2011bm spanning a period of about one year. The data establish that SN 2011bm is a spectroscopically normal SN Ic with moderately low ejecta velocities and with a very slow spectroscopic and photometric evolution (more than twice as slow as SN 1998bw). The Pan-STARRS1 retrospective detection shows that the rise time from explosion to peak was 40 days in the R band. Through an analysis of the light curve and the spectral sequence, we estimate a kinetic energy of 7-17 foe and a total ejected mass of 7-17 Mo, 5-10 Mo of which is oxygen and 0.6-0.7 Mo is 56Ni. The physical parameters obtained for SN 2011bm suggest that its progenitor was a massive star of initial mass 30-50 Mo. The profile of the forbidden oxygen lines in the nebular spectra show no evidence of a bi-polar geometry in the ejected material.

Acceleration of ions up to 20MeV/nucleon in the ultrashort, high-intensity regime

The measurements reported here provide scaling laws for the ion acceleration process in the regime of ultrashort (50 fs), ultrahigh contrast (10) and ultrahigh intensity (> 10W/cm ), never investigated previously. The scaling of the accelerated ion energies was studied by varying a number of parameters such as target thickness (down to 10nm), target material (C and Al) and laser light polar- ization (circular and linear) at 35° and normal laser incidence. A twofold increase in proton energy and an order of magnitude enhancement in ion flux have been observed over the investigated thickness range at 35° angle of incidence. Further- more, at normal laser incidence, measured peak proton energies of about 20 MeV are observed almost independently of the target thickness over a wide range (50nm- 10 µm). 1. © 2012 by Società Italiana di Fisica.

Laser-driven acceleration of ions:State of the art, perspectives and applications

The acceleration of ions with high-power lasers has been a very active field of research during the past 10 years. This paper summarizes the main results obtained in the field, detailing the mechanisms of the acceleration process and the main observed beam characteristics. Perspectives for future development of the field and current and future applications are also discussed. © 2012 by Società Italiana di Fisica.

Rethinking the Sacred and Secular Divide. Accounting and Accountability Practices in the Diocese of Ferrara (1431-1457)

Purpose – Informed by the work of Laughlin and Booth, the paper analyses the role of accounting and accountability practices within the 15th century Roman Catholic Church, more specifically within the Diocese of Ferrara (northern Italy), in order to determine the presence of a sacred-secular dichotomy. Pope Eugenius IV had embarked upon a comprehensive reform of the Church to counter the spreading moral corruption within the clergy and the subsequent disaffection with the Church by many believers. The reforms were notable not only for the Pope’s determination to restore the moral authority and power of the Church but for the essential contributions of ‘profane’ financial and accounting practices to the success of the reforms.
Design/methodology/approach – Original 15th century Latin documents and account books of the Diocese of Ferrara are used to highlight the link between the new sacred values imposed by Pope Eugenius IV’s reforms and accounting and accountability practices.
Findings – The documents reveal that secular accounting and accountability practices were not regarded as necessarily antithetical to religious values, as would be expected by Laughlin and Booth. Instead, they were seen to assume a role which was complementary to the Church’s religious mission. Indeed, they were essential to its sacred mission during a period in which the Pope sought to arrest the moral decay of the clergy and reinstate the Church’s authority. Research implications/limitations – The paper shows that the sacred-secular dichotomy cannot be considered as a priori valid in space and time. There is also scope for examining other Italian dioceses where there was little evidence of Pope Eugenius’ reforms.
Originality/value – The paper presents a critique of the sacred-secular divide paradigm by considering an under-researched period and a non Anglo-Saxon context.

Il Piano della Performance 2011-2013 dei Comuni italiani di medie e grandi dimensioni: allineamento normativo e adeguatezza programmatica in ottica economico-aziendale

Il presente lavoro intende individuare le possibili configurazioni di Piano della Performance (PdP) utilizzabili dagli enti locali, provvedendo poi a delineare il livello di distribuzione e di allineamento dei PdP 2011-2013 dei Comuni medi e grandi rispetto alle suddette configurazioni. Inoltre, verrà valutato, tramite una griglia predisposta dagli autori, il livello di adeguatezza programmatica dei Piani della Performance dei Comuni medi e grandi, al fine di confermare le configurazioni esistenti o di proporne una nuova in caso di inadeguatezza delle prime.

Italy's got talent. How Italian leading companies in confectionery industry overcame the crisis

The crisis that spread worldwide since 2007 started from the financial sector and ended to affect also real economy. This process has attracted the attention of many scholars seeking to study its causes and impacts. Notwithstanding many works on this topic, the impact of the crisis on specific industries is still rather unexplored. The present work seeks to address this issue by analyzing the confectionery industry, with particular emphasis for Italian market leaders, Ferrero S.p.A. and Perfetti Van Melle S.r.l.. The aim of the study is to assess if they have been successful in tackling the crisis, keeping a satisfactory level of profitability associated to a good financial health notwithstanding ongoing difficulties. Moreover, we seek to analyze the strategies the companies employed to survive the crisis. The concern of the paper is both quantitative and qualitative. Thus, we calculated a complete set of indicators using a specific methodology for financial statement analysis which has been conceived especially for studying Italian firms; these data have been integrated with other information retrieved from the annual reports of the companies (especially the notes to the accounts and the directors’ report). The analysis highlights that both the firms benefit from a good financial health, with Perfetti Van Melle presenting a large amount of liquidity. On the contrary, liquidity should be the main concern of Ferrero because of an excessive reliance on current liabilities. Both the firms have a good level of profitability, even if Perfetti Van Melle’s one is decreasing. The key-strategies for the success of these firms are ongoing investments in state-of-the-art plant and machinery, an increasing use of equity as the main source of funding, along with huge investments in research and advertising.

Brunetta’s reform swan song? An assessment of its success in local governments through the analysis of its tools

The work aims at assessing the success of Brunetta’s reform (Legislative Decree n. 150/2009), a far-reaching reform that aimed at improving both organizational and individual performance in Italian public administration through a specific planning and control process (the performance cycle) and most of all through two new tools, Performance Plan and Performance Report. The success of the reform is assessed, with particular emphasis on local governments, analyzing the diffusion and use of these new tools. The study has been conducted using a deductive-inductive methodology. Thus, after a study of managerial reforms in Italy and performance measurement literature, a possible model (PerformEL Model) local governments could follow to draw up Performance Plan and Report as effective tools for performance measurement has been designed (deductive phase). Performance Plans 2011-2013 and Performance Report 2011 downloaded from Italian big sized municipalities’ websites have been analyzed in the light of PerformEL Model, to assess the diffusion of the documents and their coherence with legal requirements and suggestions from literature (inductive phase). Data arising from the empirical analysis have been studied to evaluate the diffusion and the effectiveness of big sized municipalities’ Performance Plans and Reports as performance measurement tools and thus to assess the success of the reform (feedback phase). The study shows a scarce diffusion of the documents; they are mostly drew up because of their compulsoriness or to gain legitimization. The results testify the failure of Brunetta’s reform, at least with regard to local governments.

Il Piano della Performance nei Comuni medi. La proposta di una nuova configurazione per superare l’inadeguatezza delle prime applicazioni

Il D.Lgs. 150/09 ha inteso dar vita ad una “riforma organica” della PA italiana, improntandone il funzionamento a logiche di programmazione e controllo delle performance. Attorno a tale concetto la riforma ha costruito un Sistema teso a programmare, misurare, controllare, valutare e comunicare la performance degli enti. Il lavoro si focalizza sulla programmazione, e in particolare sullo strumento cardine introdotto dal D.Lgs. 150/09: il Piano della Performance (PdP). Il contributo, basato su una metodologia deduttivo-induttiva, si concentra sui comuni medi italiani, scelti in quanto statisticamente rappresentativi del livello medio di complessità degli enti locali. Sono stati oggetto di indagine i PdP pubblicati sui siti istituzionali degli enti considerati, al fine di verificarne sia il livello di aderenza alle Linee Guida (LG) emanate dalla Commissione Indipendente per la Valutazione, la Trasparenza e l’Integrità delle amministrazioni pubbliche (CIVIT) e dalla Associazione Nazionale Comuni Italiani (ANCI), sia il loro livello di adeguatezza economico-aziendale. Preliminarmente si indagherà il tema della programmazione, sotto il profilo normativo-dottrinale, concentrandosi su soggetti, processi e strumenti. Poi si sposterà il focus sul PdP: dopo aver definito obiettivi, quesiti e metodologia della ricerca, verranno esplicitate le configurazioni di PdP emergenti dalle LG CIVIT e ANCI. Verranno poi illustrati i risultati della ricerca empirica, mettendo in luce il livello di allineamento dei PdP dei comuni medi alle LG, nonché il livello di adeguatezza economico-aziendale degli stessi. Si tratteggeranno quindi alcune brevi conclusioni.

Performance management systems and Public Value Strategy: a case study

Purpose
This article aims to analyze the role of performance management systems (PMS) in supporting public value strategies.

Design/methodology/approach
This article draws on the public value dynamic model by Horner and Hutton (2010). It presents the results of a case study of implementation of a PMS model, the ‘Value Pyramid’ (VP).

Findings
The results stress the need for an improved conceptualization of PMS within public value strategy. Through experimentation using the VP, the case site was able to measure and visualize what it considered public value and reflect on the internal/external causes of both creation and destruction of public value.

Research limitations/implication
This article is limited to just one case study, although in-depth and longitudinal.

Originality/value
This article is one of the first attempting to understand the role of PMS within the public value strategy framework, answering the call of Benington and Moore (2010) to consider public value from an accounting perspective.

A new sensory organ in "primitive" molluscs (Polyplacophora Lepidopleurida), and its context in the nervous system of chitons

Introduction: Chitons (Polyplacophora) are molluscs considered to have a simple nervous system without cephalisation. The position of the class within Mollusca is the topic of extensive debate and neuroanatomical characters can provide new sources of phylogenetic data as well as insights into the fundamental biology of the organisms. We report a new discrete anterior sensory structure in chitons, occurring throughout Lepidopleurida, the order of living chitons that retains plesiomorphic characteristics.

Results: The novel "Schwabe organ" is clearly visible on living animals as a pair of streaks of brown or purplish pigment on the roof of the pallial cavity, lateral to or partly covered by the mouth lappets. We describe the histology and ultrastructure of the anterior nervous system, including the Schwabe organ, in two lepidopleuran chitons using light and electron microscopy. The oesophageal nerve ring is greatly enlarged and displays ganglionic structure, with the neuropil surrounded by neural somata. The Schwabe organ is innervated by the lateral nerve cord, and dense bundles of nerve fibres running through the Schwabe organ epithelium are frequently surrounded by the pigment granules which characterise the organ. Basal cells projecting to the epithelial surface and cells bearing a large number of ciliary structures may be indicative of sensory function. The Schwabe organ is present in all genera within Lepidopleurida (and absent throughout Chitonida) and represents a novel anatomical synapomorphy of the clade.

Conclusions: The Schwabe organ is a pigmented sensory organ, found on the ventral surface of deep-sea and shallow water chitons; although its anatomy is well understood, its function remains unknown. The anterior commissure of the chiton oesophagial nerve ring can be considered a brain. Our thorough review of the chiton central nervous system, and particularly the sensory organs of the pallial cavity, provides a context to interpret neuroanatomical homology and assess this new sense organ.

, Lexicographic Preferences in Discrete Choice Experiments: Consequences on Individual-Specific Willingness to Pay Estimates

In discrete choice experiments respondents are generally assumed to consider all of the attributes across each of the alternatives, and to choose their most preferred. However, results in this paper indicate that many respondents employ simplified lexicographic decision-making rules, whereby they have a ranking of the attributes, but their choice of an alternative is based solely on the level of their most important attribute(s). Not accounting for these simple decision-making heuristics introduces systemic errors and leads to biased point estimates, as they are a violation of the continuity axiom and a departure from the use of compensatory decision-making. In this paper the implications of lexicographic preferences are examined. In particular, using a mixed logit specification this paper investigates the sensitivity of individual-specific willingness to pay (WTP) estimates conditional on whether lexicographic decision-making rules are accounted for in the modelling of discrete choice responses. Empirical results are obtained from a discrete choice experiment that was carried out to address the value of a number of rural landscape attributes in Ireland