Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes

Metabolic stable isotope labeling is increasingly employed for accurate protein (and metabolite) quantitation using mass spectrometry (MS). It provides sample-specific isotopologues that can be used to facilitate comparative analysis of two or more samples. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has been used for almost a decade in proteomic research and analytical software solutions have been established that provide an easy and integrated workflow for elucidating sample abundance ratios for most MS data formats. While SILAC is a discrete labeling method using specific amino acids, global metabolic stable isotope labeling using isotopes such as (15)N labels the entire element content of the sample, i.e. for (15)N the entire peptide backbone in addition to all nitrogen-containing side chains. Although global metabolic labeling can deliver advantages with regard to isotope incorporation and costs, the requirements for data analysis are more demanding because, for instance for polypeptides, the mass difference introduced by the label depends on the amino acid composition. Consequently, there has been less progress on the automation of the data processing and mining steps for this type of protein quantitation. Here, we present a new integrated software solution for the quantitative analysis of protein expression in differential samples and show the benefits of high-resolution MS data in quantitative proteomic analyses.

The impact of an insecticide on insect flower visitation and pollination in an agricultural landscape

1 Pesticides are considered a threat to pollinators but little is known about the potential impacts of their widespread use on pollinators. Less still is known about the impacts on pollination, comprising the ecosystem service that pollinators provide to wildflowers and crops. 2 The present study measured flower visitation and pollination in an agricultural landscape, by placing potted flowering plants (Petunia sp.) in vine fields sprayed with a highly toxic insecticide (fenitrothion). During two sampling rounds, insect visitors to the petunias were observed and measures of pollination were recorded by counting and weighing seeds. 3 In the earlier sampling round, a lower species richness of insect visitors was observed in fields that had received an early application of insecticide. No negative impacts were found from later applications. The results obtained suggest a greater potential harm to insect pollinators and flower visitation as a result of insecticide application early in the season. 4 No reduction in pollination was found in fields that received an early insecticide application. Pollination was greater with two insecticide applications between sampling rounds rather than one application. 5 In the present study system, insecticide application had a negative effect on pollinators but a possible positive effect on pollination services. In some cases, it may be that actions for conserving biodiversity will not benefit pollination services to all plants.

Discerning policy and drivers for sustainable facilities management practice

Due to the changing nature of the facilities management (FM) profession, facilities managers are increasingly engaged with the evolving sustainability agenda in the UK and the development or uptake of sustainability policies within their organisations. This study investigates how facilities managers are engaging with the sustainability agenda and the drivers, policy issues and information they use to improve their sustainability performance management. A web based self-administered questionnaire survey of facilities managers in the UK was conducted to identify drivers and issues that influence and support good sustainable practices. A total of 268 facilities managers responded. The results indicate that legislation is the most important driver for the implementation of sustainable practices. Corporate image and Organisational ethos are also recognised. However demand for efficient monitoring, management and reporting on environmental impact is not highly rated even though the top three issues of sustainability managed by facilities managers are energy management, waste and recycling management and carbon footprint. In addition, facilities managers are expected to take ownership of activities assigned to the reduction of carbon emission. Government industries and organisation with high turnover are more likely to have a sustainability policy. Financial constraints are the main barriers while legislations are the main driver for implementing sustainability. For non-profit organisations and the charitable sector, financial constraints are no hindrance to implementing a sustainability policy. The conclusion drawn is that sustainability agendas continue to be influenced by regulated environmental issues rather than a balanced approach which takes into consideration the wider social and economic aspects of sustainability. While this scenario is far from ideal, the expectation is that the organisation will trust FM to take a vital role in delivering a comprehensive sustainability policy due to the rising tide of legislation, public scrutiny, as well as the needed business case for genuinely embracing sustainability. However, as the integration of sustainability with core business strategies is continuously evolving the emphasis on different drivers will vary from organisation to organisation as well as the responsibilities of facilities managers.

Benchmarks and the accuracy of GARCH model estimation

This paper reviews nine software packages with particular reference to their GARCH model estimation accuracy when judged against a respected benchmark. We consider the numerical consistency of GARCH and EGARCH estimation and forecasting. Our results have a number of implications for published research and future software development. Finally, we argue that the establishment of benchmarks for other standard non-linear models is long overdue.

Equipped to deal with uncertainty in climate and impacts predictions: lessons from internal peer review

The quantification of uncertainty is an increasingly popular topic, with clear importance for climate change policy. However, uncertainty assessments are open to a range of interpretations, each of which may lead to a different policy recommendation. In the EQUIP project researchers from the UK climate modelling, statistical modelling, and impacts communities worked together on ‘end-to-end’ uncertainty assessments of climate change and its impacts. Here, we use an experiment in peer review amongst project members to assess variation in the assessment of uncertainties between EQUIP researchers. We find overall agreement on key sources of uncertainty but a large variation in the assessment of the methods used for uncertainty assessment. Results show that communication aimed at specialists makes the methods used harder to assess. There is also evidence of individual bias, which is partially attributable to disciplinary backgrounds. However, varying views on the methods used to quantify uncertainty did not preclude consensus on the consequential results produced using those methods. Based on our analysis, we make recommendations for developing and presenting statements on climate and its impacts. These include the use of a common uncertainty reporting format in order to make assumptions clear; presentation of results in terms of processes and trade-offs rather than only numerical ranges; and reporting multiple assessments of uncertainty in order to elucidate a more complete picture of impacts and their uncertainties. This in turn implies research should be done by teams of people with a range of backgrounds and time for interaction and discussion, with fewer but more comprehensive outputs in which the range of opinions is recorded.

Counting in Egyptian children with Down Syndrome

This exploratory study is concerned with the performance of Egyptian children with Down syndrome on counting and error detection tasks and investigates how these children acquire counting. Observations and interviews were carried out to collect further information about their performance in a class context. Qualitative and quantitative analysis suggested a notable deficit in counting in Egyptian children with Down syndrome with none of the children able to recite the number string up to ten or count a set of five objects correctly. They performed less well on tasks which added more load on memory. The tentative finding of this exploratory study supported previous research findings that children with Down syndrome acquire counting by rote and links this with their learning experiences.

Does stakeholder pressure influence corporate GHG emissions reporting? Empirical evidence from Europe

Purpose – The purpose of this paper is to seek to shed light on the practice of incomplete corporate disclosure of quantitative Greenhouse gas (GHG) emissions and investigates whether external stakeholder pressure influences the existence, and separately, the completeness of voluntary GHG emissions disclosures by 431 European companies. Design/methodology/approach – A classification of reporting completeness is developed with respect to the scope, type and reporting boundary of GHG emissions based on the guidelines of the GHG Protocol, Global Reporting Initiative and the Carbon Disclosure Project. Logistic regression analysis is applied to examine whether proxies for exposure to climate change concerns from different stakeholder groups influence the existence and/or completeness of quantitative GHG emissions disclosure. Findings – From 2005 to 2009, on average only 15 percent of companies that disclose GHG emissions report them in a manner that the authors consider complete. Results of regression analyses suggest that external stakeholder pressure is a determinant of the existence but not the completeness of emissions disclosure. Findings are consistent with stakeholder theory arguments that companies respond to external stakeholder pressure to report GHG emissions, but also with legitimacy theory claims that firms can use carbon disclosure, in this case the incomplete reporting of emissions, as a symbolic act to address legitimacy exposures. Practical implications – Bringing corporate GHG emissions disclosure in line with recommended guidelines will require either more direct stakeholder pressure or, perhaps, a mandated disclosure regime. In the meantime, users of the data will need to carefully consider the relevance of the reported data and develop the necessary competencies to detect and control for its incompleteness. A more troubling concern is that stakeholders may instead grow to accept less than complete disclosure. Originality/value – The paper represents the first large-scale empirical study into the completeness of companies’ disclosure of quantitative GHG emissions and is the first to analyze these disclosures in the context of stakeholder pressure and its relation to legitimation.

The role of big data in governance: a regulatory and legal perspective of analytics in global financial services

This paper discusses how global financial institutions are using big data analytics within their compliance operations. A lot of previous research has focused on the strategic implications of big data, but not much research has considered how such tools are entwined with regulatory breaches and investigations in financial services. Our work covers two in-depth qualitative case studies, each addressing a distinct type of analytics. The first case focuses on analytics which manage everyday compliance breaches and so are expected by managers. The second case focuses on analytics which facilitate investigation and litigation where serious unexpected breaches may have occurred. In doing so, the study focuses on the micro/data to understand how these tools are influencing operational risks and practices. The paper draws from two bodies of literature, the social studies of information systems and finance to guide our analysis and practitioner recommendations. The cases illustrate how technologies are implicated in multijurisdictional challenges and regulatory conflicts at each end of the operational risk spectrum. We find that compliance analytics are both shaping and reporting regulatory matters yet often firms may have difficulties in recruiting individuals with relevant but diverse skill sets. The cases also underscore the increasing need for financial organizations to adopt robust information governance policies and processes to ease future remediation efforts.

Iron Concentrations in Breast Milk and Selected Maternal Factors of Human Milk Bank Donors

The aim of this study was to evaluate the relationship between iron concentration in mature breast milk and characteristics of 136 donors of a Brazilian milk bank. Iron, vitamin A, zinc, and copper concentrations were assessed in human milk and maternal blood. Data were collected on maternal anthropometrics, obstetric, socioeconomic, demographic, and lifestyle factors. Iron, zinc, and copper in milk and zinc and copper in blood were detected by spectrophotometry. Vitamin A in milk and blood was determined by high-performance liquid chromatography. Hemoglobin was measured by electronic counting and serum iron and ferritin by colorimetry and chemoluminescence, respectively. Transferrin and ceruloplasmin were determined by nephelometry. According to multivariate linear regression analysis, iron in milk was positively associated with vitamin A in milk and with smoking but negatively associated with timing of breast milk donation (P < .001). These results indicate that iron concentration in milk of Brazilian donors may be influenced by nutritional factors and smoking. J Hum Lact. 26(2):175-179

Culture medium for isolating chitinolytic bacteria from seawater and plankton

Chitin degradation is a key step in the cycling of nutrients in marine ecosystems and chitinolytic bacteria are the primary agents of this process. Chitinases, produced by bacteria, have potential applications in agriculture, medicine and in a wide range of biotechnological processes. We utilized a simple, rapid and cost-effective method of colloidal chitin preparation and a culture medium, in which colloidal chitin is the sole carbon source for the purpose of counting and isolating chitinolytic bacteria from seawater and plankton. This culture medium could be useful to isolate bacteria with the ability to produce extracellular chitinases for biotechnological applications.

Software reuse: The Brazilian industry scenario

This paper aims at identifying some of the key factors in adopting an organization-wide software reuse program. The factors are derived from practical experience reported by industry professionals, through a survey involving 57 Brazilian small, medium and large software organizations. Some of them produce software with commonality between applications, and have mature processes, while others successfully achieved reuse through isolated, ad hoe efforts. The paper compiles the answers from the survey participants, showing which factors were more associated with reuse success. Based on this relationship, a guide is presented, pointing out which factors should be more strongly considered by small, medium and large organizations attempting to establish a reuse program. (C) 2007 Elsevier Inc. All rights reserved.

An aspect-oriented reference architecture for Software Engineering Environments

Reusable and evolvable Software Engineering Environments (SEES) are essential to software production and have increasingly become a need. In another perspective, software architectures and reference architectures have played a significant role in determining the success of software systems. In this paper we present a reference architecture for SEEs, named RefASSET, which is based on concepts coming from the aspect-oriented approach. This architecture is specialized to the software testing domain and the development of tools for that domain is discussed. This and other case studies have pointed out that the use of aspects in RefASSET provides a better Separation of Concerns, resulting in reusable and evolvable SEEs. (C) 2011 Elsevier Inc. All rights reserved.

Price setting and macroeconomic variables: evidence from Brazilian CPI

Esta tese investiga as estratégias de precificação em ambientes macroeconômicos distintos, utilizando uma base de dados única para o IPC da Fundação Getulio Vargas. A base de dados primária consiste em um painel de dados individuais para bens e serviços representando 100% do IPC para o período de 1996 a 2008. Durante este período, diversos eventos produziram uma variabilidade macroeconômica substancial no Brasil: duas crises em países emergentes, uma mudança de regime cambial e monetário, racionamento de energia, uma crise de expectativas eleitorais e um processo de desinflação. Como consequência, a inflação, a incerteza macroeconômica, a taxa de câmbio e o produto exibiram uma variação considerável no período. No primeiro capítulo, nós descrevemos a base de dados e apresentamos as principais estatísticas de price-setting para o Brasil. Em seguida, nos capítulos 2 e 3, nos construímos as séries de tempo destas estatísticas e das estatísticas de promoções, e as relacionamos com as variáveis macroeconômicas utilizando análises de regressões. Os resultados indicam que há uma relação substancial entre as estatísticas de price-setting e o ambiente macroeconômico para a economia brasileira.

Comparison and analysis of corporate social responsibility (CSR) reports of the top five companies ranked on the 2013 CSR RepTrak

In the 1970s, Corporate Social Responsibility (CSR) was discussed by Nobel laureate Milton Friedman in his article “The Social Responsibility of Business Is to Increase Its Profits.” (Friedman, 1970). His view on CSR was contemptuous as he referred to it as “hypocritical window-dressing” a reflection of the view of Corporate America on CSR back then. For a long time short-term maximization of shareholder value was the only maxim for top management across industries and companies. Over the last decade, CSR has become a more important and relevant factor of a company’s reputation, shifting the discussion from whether CSR is necessary to how best CSR commitments should be done (Smith, 2003). Inevitably, companies do have an environmental, social and economic impact, thereby imposing social costs on current and future generations. In 2013, 50 of the world biggest companies have been responsible for 73 percent of the total carbon dioxide (CO2) emission (Global 500 Climate Change Report 2013). Post et al. (2002) refer to these social costs as a company’s need to retain its “license to operate”. In the late 1990s, CSR reporting was nearly unknown, which drastically changed during the last decade. Allen White, co-founder of the Global Reporting Initiative (GRI), said that CSR reporting”… has evolved from the extraordinary to the exceptional to the expected” (Confino, 2013). In confirmation of this, virtually all of the world’s largest 250 companies report on CSR (93%) and reporting by now appears to be business standard (KPMG, 2013). CSR reports are a medium for transparency which may lead to an improved company reputation (Noked, 2013; Thorne et al, 2008; Wilburn and Wilburn, 2013). In addition, it may be used as part of an ongoing shareholder relations campaign, which may prevent shareholders from submitting Environmental and Social (E&S)1 proposals (Noked, 2013), based on an Ernst & Young report 1 The top five E&S proposal topic areas in 2013 were: 1. Political spending/ lobbying; 2. Environmental sustainability; 3. Corporate diversity/ EEO; 4.Labor/ human rights and 5. Animal testing/ animal welfare. Three groups of environmental sustainability proposal topics of sub-category number two (environmental sustainability) 6 2013, representing the largest category of shareholder proposals submitted. PricewaterhouseCoopers (PwC) even goes as far as to claim that CSR reports are “…becoming critical to a company’s credibility, transparency and endurance.” (PwC, 2013).