Electron Capture Dissociation Mass Spectrometry of Tyrosine Nitrated Peptides

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification.Here, we have investigated the electron capture dissociation (ECD) and collision-induced association (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains

ICT-based solution approach for collaborative delivery of customised products

© 2016 Taylor & Francis. Growing interest on business collaboration motivates todays industries, especially small and medium enterprises (SMEs) to establish and manage dynamic and non-hierarchical business networks to respond to market opportunities with added business benefits. This business environment requires concurrent work and real-time information sharing between key business partners in order to design and develop customised products. The use of traditional communication media such as e-mail, phone and fax is not satisfactory to get real-time information and is time-consuming and most often ineffective. In such environments, an Information and Communication Technology (ICT)/Web-based technology supports real-time information sharing among networked SMEs for the collaborative design and manufacturing of customised products. This study proposes an innovative ICT platform supporting SMEs collaboration, through Web and the Internet of Things technologies, which follows the Net-Challenge conceptual approach and methodological guidelines for SMEs to form and operate virtual organisations for the collaborative development and delivery of customised products. The ICT Platform was assessed in three different industry domains, namely the textile and apparel, the footwear and the machine tools, respectively. This ICT solution promotes collaboration, with substantial advantages for SMEs including the reduction of costs and delivery time and improvement of the innovation potential

Statistical analysis of the sampling design: FishPi case study on the biological sampling of the European hake fishery

FishPi is a pilot project financed through an European grant (MARE/2014/19) aiming to strengthen regional coordination in the area of fisheries data collection. This project includes four case studies, one of which aims at analyzing alternative sampling plans for fisheries operating on Northern & Southern hake stocks. The case study analyzes a variety of sampling design scenarios, from Simple Random Sampling to combinations of stratified sampling designs (by country, by port, by quarter…), using anonymised landings data from logbooks and sales notes (2013-2014). The results were compared regarding bias and precision to evaluate the best approach. The most precise estimates of total catch were obtained in scenarios stratified by port and, secondly, by port and country and by port and quarter. The general conclusion was that regional sampling designs stratified by port provided improved precision in this fishery. Apart from statistical considerations, this conclusion was also discussed under other points of view to give a feasibility perspective showing that coverage by country, and also by domain (stock), would be compromised if regional design is simply based on statistical analyses. Efficiency and precision of sampling were found to be highly sensitive to the sampling assumptions and in general countries with smaller contributions to overall landings of hake would see their sampling plans reduced, compromising other requirements for advice such as those related to other stocks or local management measures established by National governments. Hence further analyses are being considered that integrate biometrics, cost-benefit aspects, and concurrent or single-stock sampling strategies

Report of the Working Group on Commercial Catches (WGCATCH)

The Working Group on Commercial Catches (WGCATCH), chaired by Hans Gerritsen (Ireland) and Nuno Prista (Sweden), met in Lisbon, Portugal, 9–13 November 2015. WGCATCH is responsible for documenting national fishery sampling schemes, establishing best practice and guidelines on sampling and estimation procedures, and providing advice on other uses of fishery data. The meeting was attended by 30 participants from 15 countries. The group addressed a large number of terms of reference and the meeting was con-ducted through presentations, discussions and analysis of questionnaires. The main terms of reference were addressed in subgroups. The report is structured directly along the terms of reference and the main outcomes are listed below. Data collection schemes for small-scale fisheries WGCATCH provided descriptions of national small-scale fisheries through question-naires. An overview was obtained on the current data collection methods. Two major approaches were identified - census (e.g., sales, logbooks) and sampling methods (e.g., catch surveys) - and their main pros and cons were discussed. In most cases, specific sampling approaches are needed for these fisheries. The group developed a work plan to establish good-practice guidelines. Analysis of case studies of commercial fishery sampling designs and estimation Case studies of sampling designs and estimation involving megrim in divisions 7-8 were presented. A common theme is that issues with practical implementation of prob-ability-based sampling remain. WGCATCH summarized the main issues and provided a set of possible solutions. The group also provided guidance on dealing with previous data collected under métier-based sampling designs. Simulation models to investigate survey designs Several simulation studies were presented, most of them outlining the work of fishPi project (funded under MARE/2014/19) in evaluating regional sampling designs. A crit-ical review was carried out and WGCATCH produced general considerations and guidelines. WGCATCH recommends that these are taken into account when analysing the results of simulations of regional sampling design at RCM level. The affect of the landing obligation on catch sampling opportunities The affects on sampling and data quality of the current implementation of the landing obligation in the Baltic were reviewed. The group found that refusal rates for observer trips have increased to nearly 100% in at least one country, while in many other coun-tries on-board observer programmes did not suffer noticeable changes. WGCATCH established that the catches below the minimum size cannot be accurately estimated by sampling the landings below the minimum size because an unknown proportion of the catches may be discarded. The group also reiterated that it is important that the logbooks distinguish landings below and above the minimum size. Publication on statistically sound sampling schemes WGCATCH drafted detailed plans to produce a peer-reviewed paper in 2016. The pa-per will provide a synthesis of the evolution of sampling design towards best practice, illustrated with a number of concise case studies. Estimation procedures in the Regional Database (RDB) The work of WKRDB 2015 presented alongside existing and planned estimation pro-cedures in the RDB. Current work by Norway on a software package that will allow design-based estimation and optimization for stock assessment purposes was also pre-sented. The advantages of ensuring compatibility of this new software with the devel-opments currently planned for RDB-FishFrame are underscored. Repository of resources relevant to catch sampling WGCATCH initiated a repository with key resources; putting them into context with brief descriptions or review of each report, paper, book, website, software package etc. The intention is for this repository to be made available online by ICES. Sampling of incidental bycatches WGCATCH agreed to start routine documentation of sampling practices for bycatches of protected, endangered and threatened species (PETS) and rare fish species as well as routine evaluation of the limitations of current methods for collection and analysis. Training course on Design and Analysis of Statistical Sound catch sampling pro-grammes WGCATCH considered continuous training and expertise on sampling design, estima-tion and simulation to be the basis for successful implementation of statistical sound catch sampling programs. A new ICES Training Course in Design and Analysis of Sta-tistical Sound will take place at ICES HQ in Copenhagen, 12–16 September 2016. WGCATCH recommends that RCMs promote the attendance of these meetings among all MS involved

Intratumoural and peripheral blood lymphocyte subsets in patients with metastatic renal cell carcinoma undergoing interleukin-2 based immunotherapy: association to objective response and survival

The aim of the present study was to analyse lymphocyte subsets in consecutive peripheral blood samples and consecutive tumour tissue core needle biopsies performed before and during interleukin-2 based immunotherapy, and to correlate the findings with objective response and survival. Twenty-six patients with metastatic renal cell carcinoma were treated with low dose s.c. interleukin-2, interferon-α and histamine. A total of 250 blood samples and 62 core needle biopsies from 23 and 19 of these patients, respectively, were analysed. After 2 weeks of treatment, a significant positive correlation between absolute number of peripheral blood lymphocytes (P=0.028), CD3 (P=0.017), CD57 (P=0.041) and objective response was demonstrated. There was no correlation between any peripheral blood leukocyte subsets and survival. Cytotoxicity of peripheral blood mononuclear cells was not correlated to objective response or survival. Within the tumour tissue at baseline, a significant positive correlation between CD4 (P=0.027), CD8 (P=0.028), CD57 (P=0.007) and objective response was demonstrated. After one month of immunotherapy, a significant positive correlation between intratumoral CD3 (P=0.026), CD8 (P=0.015), CD57 (P=0.009) and objective response was demonstrated. A significant positive correlation between intratumoral baseline CD4 (P=0.047), baseline CD57 (P=0.035), CD3 at one month (P=0.049) and survival was demonstrated. These data provide novel in vivo evidence of the possible contribution of lymphocyte subsets in the tumour reduction in responding patients during interleukin-2 based immunotherapy. Confirmation of the results requires further studies including a larger number of patients

Identification and Characterization of Alternative Promoters, Transcripts and Protein Isoforms of Zebrafish R2 Gene

Ribonucleotide reductase (RNR) is the rate-limiting enzyme in the de novo synthesis of deoxyribonucleoside triphosphates. Expression of RNR subunits is closely associated with DNA replication and repair. Mammalian RNR M2 subunit (R2) functions exclusively in DNA replication of normal cells due to its S phase-specific expression and late mitotic degradation. Herein, we demonstrate the control of R2 expression through alternative promoters, splicing and polyadenylation sites in zebrafish. Three functional R2 promoters were identified to generate six transcript variants with distinct 5′ termini. The proximal promoter contains a conserved E2F binding site and two CCAAT boxes, which are crucial for the transcription of R2 gene during cell cycle. Activity of the distal promoter can be induced by DNA damage to generate four transcript variants through alternative splicing. In addition, two novel splice variants were found to encode distinct N-truncated R2 isoforms containing residues for enzymatic activity but no KEN box essential for its proteolysis. These two N-truncated R2 isoforms remained in the cytoplasm and were able to interact with RNR M1 subunit (R1). Thus, our results suggest that multilayered mechanisms control the differential expression and function of zebrafish R2 gene during cell cycle and under genotoxic stress

Understanding the effects of a decentralized budget on physicians' compliance with guidelines for statin prescription – a multilevel methodological approach

<p>Abstract</p> <p>Background</p> <p>Official guidelines that promote evidence-based and cost-effective prescribing are of main relevance for obvious reasons. However, to what extent these guidelines are followed and their conditioning factors at different levels of the health care system are still insufficiently known.</p> <p>In January 2004, a decentralized drug budget was implemented in the county of Scania, Sweden. Focusing on lipid-lowering drugs (i.e., statins), we evaluated the effect of this intervention across a 25-month period. We expected that increased local economic responsibility would promote prescribing of recommended statins.</p> <p>Methods</p> <p>We performed two separate multilevel regression analyses; on 110 827 individual prescriptions issued at 136 <it>publicly</it>-administered health care centres (HCCs) nested within 14 administrative areas (HCAs), and on 72 012 individual prescriptions issued by 115 <it>privately</it>-administered HCCs. Temporal trends in the prevalence of prescription of recommended statins were investigated by random slope analysis. Differences (i.e., variance) between HCCs and between HCAs were expressed by median odds ratio (MOR).</p> <p>Results</p> <p>After the implementation of the decentralized drug budget, adherence to guidelines increased continuously. At the end of the observation period, however, practice variation remained high. Prescription of recommended statins presented a high degree of clustering within both publicly (i.e., MOR_HCC= 2.18 and MOR_HCA= 1.31 respectively) and privately administered facilities (MOR_HCC= 3.47).</p> <p>Conclusion</p> <p>A decentralized drug budget seems to promote adherence to guidelines for statin prescription. However, the high practice differences at the end of the observation period may reflect inefficient therapeutic traditions, and indicates that rational statin prescription could be further improved.</p