Networks from gene expression time series: characterization of correlation patterns

This paper describes characteristic features of networks reconstructed from gene expression time series data. Several null models are considered in order to discriminate between informations embedded in the network that are related to real data, and features that are due to the method used for network reconstruction (time correlation).Comment: 10 pages, 3 BMP figures, 1 Table. To appear in Int. J. Bif. Chaos, July 2007, Volume 17, Issue

Genetic analysis of multiple synchronous lesions of the colon adenoma–carcinoma sequence

The colorectal adenoma–carcinoma sequence represents a well-known paradigm for the sequential development of cancer driven by the accumulation of genomic defects. Although the colorectal adenoma–carcinoma sequence is well investigated, studies about tumours of different dignity co-existent in the same patient are seldom. In order to address the distribution of genetic alterations in different lesions of the same patient, we coincidently investigated carcinomas, adenomas and aberrant crypt foci in patients with sporadic colon cancer. By utilizing polymerase chain reaction, single-strand conformation polymorphism, heteroduplex-analysis, restriction fragment length polymorphism, protein truncation test and sequencing techniques we looked for mutations and microsatellite instability of APC, H- ras, K- ras, p53, DCC and the DNA repair genes hMLH1/hMSH2. In accordance with the suggested adenoma–carcinoma sequence of the colon, four patients reflected the progressive accumulation of genetic defects in synchronously appearing tumours during carcinogenesis. However, two patients with non-hereditary malignomas presented different genetic instabilities in different but synchronously appearing tumours suggesting non-clonal growth under almost identical conditions of the environment. Thus, sporadically manifesting multiple lesions of the colon were not necessarily driven by similar genetic mechanisms. Premalignant lesions may transform into malignant tumours starting from different types of genetic instability, which indicates independent and simultaneous tumorigenesis within the same organ. © 2000 Cancer Research Campaig

Time-domain characterization and correction of on-chip distortion of control pulses in a quantum processor

We introduce Cryoscope, a method for sampling on-chip baseband pulses used to dynamically control qubit frequency in a quantum processor. We specifically use Cryoscope to measure the step response of the dedicated flux control lines of two-junction transmon qubits in circuit QED processors with the temporal resolution of the room-temperature arbitrary waveform generator producing the control pulses. As a first application, we iteratively improve this step response using optimized real-time digital filters to counter the linear-dynamical distortion in the control line, as needed for high-fidelity, repeatable one- and two-qubit gates based on dynamical control of qubit frequency

Editor's Choice - Infective Native Aortic Aneurysms: A Delphi Consensus Document on Terminology, Definition, Classification, Diagnosis, and Reporting Standards.

There is no consensus regarding the terminology, definition, classification, diagnostic criteria, and algorithm, or reporting standards for the disease of infective native aortic aneurysm (INAA), previously known as mycotic aneurysm. The aim of this study was to establish this by performing a consensus study. The Delphi methodology was used. Thirty-seven international experts were invited via mail to participate. Four two week Delphi rounds were performed, using an online questionnaire, initially with 22 statements and nine reporting items. The panellists rated the statements on a five point Likert scale. Comments on statements were analysed, statements revised, and results presented in iterative rounds. Consensus was defined as ≥ 75% of the panel selecting "strongly agree" or "agree" on the Likert scale, and consensus on the final assessment was defined as Cronbach's alpha coefficient > .80. All 38 panellists completed all four rounds, resulting in 100% participation and agreement that this study was necessary, and the term INAA was agreed to be optimal. Three more statements were added based on the results and comments of the panel, resulting in a final 25 statements and nine reporting items. All 25 statements reached an agreement of ≥ 87%, and all nine reporting items reached an agreement of 100%. The Cronbach's alpha increased for each consecutive round (round 1 = .84, round 2 = .87, round 3 = .90, and round 4 = .92). Thus, consensus was reached for all statements and reporting items. This Delphi study established the first consensus document on INAA regarding terminology, definition, classification, diagnostic criteria, and algorithm, as well as reporting standards. The results of this study create essential conditions for scientific research on this disease. The presented consensus will need future amendments in accordance with newly acquired knowledge

Connecting wastes to resources for clean technologies in the chlor-alkali industry: a life cycle approach

Our current economic model is experiencing increasing demand and increasing pressure on resource utilisation, as valuable materials are lost as waste. Moving towards a circular economy and supporting efficient resource utilisation is essential for protecting the environment. The chlor-alkali industry is one of the largest consumers of salt, and efforts have been made to reduce its electricity use. Furthermore, KCl mining wastes have received increasing attention because they can be transformed into value-added resources. This work studies the influence of using different salt sources on the environmental sustainability of the chlor-alkali industry to identify further improvement opportunities. Rock salt, solar salt, KCl waste salt, vacuum salt and solution-mined salt were studied. Membrane cells in both bipolar and monopolar configurations were studied and compared to the emergent oxygen-depolarised cathode (ODC) technology. Life cycle assessment was applied to estimate the cradle-to-gate environmental impacts. The natural resource (NR) requirements and the environmental burdens (EBs) to the air and water environments were assessed. The total NR and EB requirements were reduced by 20% when vacuum salt was replaced with KCl. Moreover, the environmental impacts estimated for the monopolar membrane using KCl were comparable to those generated for the bipolar membrane using VS. The difference between the monopolar and bipolar scenarios (17%) was slightly higher than that between the bipolar and ODC technologies (12%). This work demonstrates the importance of studying every life cycle stage in a chemical process and the environmental benefit of applying a circular economy, even in energy intensive industries such as the chlor-alkali industry.This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO), Project CTM2013-43539-R. The authors are grateful for this funding