Predicting Cell Cycle Regulated Genes by Causal Interactions

The fundamental difference between classic and modern biology is that technological innovations allow to generate high-throughput data to get insights into molecular interactions on a genomic scale. These high-throughput data can be used to infer gene networks, e. g., the transcriptional regulatory or signaling network, representing a blue print of the current dynamical state of the cellular system. However, gene networks do not provide direct answers to biological questions, instead, they need to be analyzed to reveal functional information of molecular working mechanisms. In this paper we propose a new approach to analyze the transcriptional regulatory network of yeast to predict cell cycle regulated genes. The novelty of our approach is that, in contrast to all other approaches aiming to predict cell cycle regulated genes, we do not use time series data but base our analysis on the prior information of causal interactions among genes. The major purpose of the present paper is to predict cell cycle regulated genes in S. cerevisiae. Our analysis is based on the transcriptional regulatory network, representing causal interactions between genes, and a list of known periodic genes. No further data are used. Our approach utilizes the causal membership of genes and the hierarchical organization of the transcriptional regulatory network leading to two groups of periodic genes with a well defined direction of information flow. We predict genes as periodic if they appear on unique shortest paths connecting two periodic genes from different hierarchy levels. Our results demonstrate that a classical problem as the prediction of cell cycle regulated genes can be seen in a new light if the concept of a causal membership of a gene is applied consequently. This also shows that there is a wealth of information buried in the transcriptional regulatory network whose unraveling may require more elaborate concepts than it might seem at first.

Children making sense of science

Abstract This study explored the effects that the incorporation of nature of science (NoS) activities in the primary science classroom had on children’s perceptions and understanding of science. We compared children’s ideas in four classes by inviting them to talk, draw and write about what science meant to them: two of the classes were taught by ‘NoS’ teachers who had completed an elective nature of science (NoS) course in the final year of their Bachelor of Education (B.Ed) degree. The ‘non-NoS’ teachers who did not attend this course taught the other two classes. All four teachers had graduated from the same initial teacher education institution with similar teaching grades and all had carried out the same science methods course during their B.Ed programme. We found that children taught by the teachers who had been NoS-trained developed more elaborate notions of nature of science, as might be expected. More importantly, their reflections on science and their science lessons evidenced a more in-depth and sophisticated articulation of the scientific process in terms of scientists “trying their best” and “sometimes getting it wrong” as well as “getting different answers”. Unlike children from non-NoS classes, those who had engaged in and reflected on NoS activities talked about their own science lessons in the sense of ‘doing science’. These children also expressed more positive attitudes about their science lessons than those from non-NoS classes. We therefore suggest that there is added value in including NoS activities in the primary science curriculum in that they seem to help children make sense of science and the scientific process, which could lead to improved attitudes towards school science. We argue that as opposed to considering the relevance of school science only in terms of children’s experience, relevance should include relevance to the world of science, and NoS activities can help children to link school science to science itself.

Decadence in the Forest: Smyth's Der Wald in its Critical Context

Ethel Smyth’s opera, Der Wald, met with mixed reactions at its premiere in Berlin in 1902. Many factors contributed to this, not least, as Smyth herself observed, anti-British sentiment in Germany following the second Boer War. One might have expected that the reception of the opera at its British premiere on 18 July at Covent Garden might have been more positive, but even here critical opinion was divided. Even positive reviews were not free from gender discrimination, and other reviews condemned the opera for being too German or Wagnerian. What was meant by ‘Wagnerian’? This article answers the question in three ways. Firstly, I argue that ‘Wagnerian’ meant not a leitmotif-filled, through-composed work (as distinct from a number opera), but simply a lyrical drama; for British audiences the model for this was Tannhäuser or Lohengrin, not the Ring or Tristan. Secondly, taking this definition on board, I analyse the musical language of the opera, in particular the key structure. The central duet sung by the doomed lovers, Heinrich and Röschen, is in F major, almost the furthest possible distance from the home key of the opera (E major), which characterizes the forest and ‘nature’ in general; by contrast, the next scene, where the Kundry-like Iolanthe attempts to seduce Heinrich (a crucial reversal of the more conventional power relations of the love duet), sees a return to the home key. Thirdly, I set the hermeneutical implications of this reversal in the context of the decadent movement, with which late nineteenth-century Wagnerism was associated, and which, following the conviction of Oscar Wilde in 1895, was discredited. Der Wald thus failed because of its ‘guilt by association’ with an aesthetic that had fallen into disrepute.

A hypercyclic finite rank perturbation of a unitary operator

A unitary operator V and a rank 2 operator R acting on a Hilbert space H are constructed such that V + R is hypercyclic. This answers affirmatively a question of Salas whether a finite rank perturbation of a hyponormal operator can be supercyclic.

A virtual surgery in general practice: evaluation of a novel undergraduate virtual patient learning package

Background: A suite of 10 online virtual patients developed using the IVIMEDS ‘Riverside’ authoring tool has been introduced into our undergraduate general practice clerkship. These cases provide a multimedia-rich experience to students. Their interactive nature promotes the development of clinical reasoning skills such as discriminating key clinical features, integrating information from a variety of sources and forming diagnoses and management plans.

Aims: To evaluate the usefulness and usability of a set of online virtual patients in an undergraduate general practice clerkship.
Method: Online questionnaire completed by students after their general practice placement incorporating the System Usability Scale questionnaire.

Results: There was a 57% response rate. Ninety-five per cent of students agreed that the online package was a useful learning tool and ranked virtual patients third out of six learning modalities. Questions and answers and the use of images and videos were all rated highly by students as useful learning methods. The package was perceived to have a high level of usability among respondents.

Conclusion: Feedback from students suggest that this implementation of virtual patients, set in primary care, is user friendly and rated as a valuable adjunct to their learning. The cost of production of such learning resources demands close attention to design.

Older people and legal advice – the need for joined up and creative approaches

This paper reports the findings from research conducted with older people in Northern
Ireland which investigated whether their needs for legal information and advice were
being met. One of the unique aspects of the research involved investigating the
potential of the internet as a possible source for advising older people in relation to
legal problems. The findings suggest that online legal information may frequently assist
older people in identifying potential answers to their legal questions, but may not be an
adequate substitute for personal communication and advice. The research also
highlights the need for professionals to work together to meet the needs of older
persons for legal advice and to safeguard their interests. Such ‘joined up’ approaches
are particularly important, for example at the point of dementia diagnosis, where
information sharing between health and social care professionals may significantly
promote the legal and welfare interests of older people at a vulnerable point in their
lives. This paper therefore turns to work by university-based legal clinics in the United
States, such as the Elder Law Clinic at Pennsylvania State University, where social
work or healthcare professionals, lawyers and law students collaborate to support older
people in their search for resolution of legal problems.

Interlocking directorates and conflicts of interest: The Rotterdamsche Bankvereeniging, Müller & Co. and the Dutch financial crisis of the 1920s

How can interlocking directorates cause financial instability for universal banks? A detailed history of the Rotterdamsche Bankvereeninging in the 1920s answers this question in a case study. This large commercial bank adopted a new German-style universal banking business model from the early 1910s, sharing directors with the firms it financed as a means of controlling its interests. Then, in 1924, it required assistance from the Dutch state in order to survive a bank run brought on by public concerns over its close ties with Müller & Co., a trading conglomerate that suffered badly in the economic downturn of the early 1920s. Using a new narrative history combined with an interpretive model, this article shows how the interlocking directorates between the bank and this major client, and in particular the direction of influence of these interlocks, resulted in a conflict of interest that could not be easily overcome.

Knowledge and perceived competence among nurses caring for the dying in long-term care homes

Background: The quality of care provided to dying long-term care (LTC) residents is often inadequate, which may be due to the lack of formal training that LTC staff receive in palliative care (PC). This cross-sectional study assessed PC knowledge and self-efficacy in ability to provide PC in a sample of registered nurses working in LTC homes. Method: A survey was conducted in four LTC homes in October 2009 to June 2010. Nursing staff knowledge of PC was evaluated using the Palliative Care Quiz for Nurses (PCQN). The Self-Efficacy in End-of-Life Care Survey (S-EOLC) was used to measure nursing staff confidence in their ability to provide PC. Findings: Close to 60% of the nursing staff participated (69 of 119). The participants did not score highly on the PCQN: the average correct score ranged from 52.50% to 63.41% across the homes. There were no significant differences between the homes for the mean number of correct responses on the PCQN (P=0.329) or mean scores for the three S-EOLC subscales. Rank ordering of the percentage of correct PCQN answers by item and LTC home demonstrated that similar misconceptions were held across homes. Conclusion: Despite their confidence in PC practice, the participants' PC knowledge gap reveals a need for PC training for staff working in LTC homes. The PC education and training provided should both include a gerontological perspective and address the expertise and knowledge already held by staff.

Robust food supply supply chains:An integrated framework for vulnerability assessment and disturbance management

The operation of supply chains (SCs) has for many years been focused on efficiency, leanness and responsiveness. This has resulted in reduced slack in operations, compressed cycle times, increased productivity and minimised inventory levels along the SC. Combined with tight tolerance settings for the realisation of logistics and production processes, this has led to SC performances that are frequently not robust. SCs are becoming increasingly vulnerable to disturbances, which can decrease the competitive power of the entire chain in the market. Moreover, in the case of food SCs non-robust performances may ultimately result in empty shelves in grocery stores and supermarkets.
The overall objective of this research is to contribute to Supply Chain Management (SCM) theory by developing a structured approach to assess SC vulnerability, so that robust performances of food SCs can be assured. We also aim to help companies in the food industry to evaluate their current state of vulnerability, and to improve their performance robustness through a better understanding of vulnerability issues. The following research questions (RQs) stem from these objectives:
RQ1: What are the main research challenges related to (food) SC robustness?
RQ2: What are the main elements that have to be considered in the design of robust SCs and what are the relationships between these elements?
RQ3: What is the relationship between the contextual factors of food SCs and the use of disturbance management principles?
RQ4: How to systematically assess the impact of disturbances in (food) SC processes on the robustness of (food) SC performances?
To answer these RQs we used different methodologies, both qualitative and quantitative. For each question, we conducted a literature survey to identify gaps in existing research and define the state of the art of knowledge on the related topics. For the second and third RQ, we conducted both exploration and testing on selected case studies. Finally, to obtain more detailed answers to the fourth question, we used simulation modelling and scenario analysis for vulnerability assessment.
Main findings are summarised as follows.
Based on an extensive literature review, we answered RQ1. The main research challenges were related to the need to define SC robustness more precisely, to identify and classify disturbances and their causes in the context of the specific characteristics of SCs and to make a systematic overview of (re)design strategies that may improve SC robustness. Also, we found that it is useful to be able to discriminate between varying degrees of SC vulnerability and to find a measure that quantifies the extent to which a company or SC shows robust performances when exposed to disturbances.
To address RQ2, we define SC robustness as the degree to which a SC shows an acceptable performance in (each of) its Key Performance Indicators (KPIs) during and after an unexpected event that caused a disturbance in one or more logistics processes. Based on the SCM literature we identified the main elements needed to achieve robust performances and structured them together to form a conceptual framework for the design of robust SCs. We then explained the logic of the framework and elaborate on each of its main elements: the SC scenario, SC disturbances, SC performance, sources of food SC vulnerability, and redesign principles and strategies.
Based on three case studies, we answered RQ3. Our major findings show that the contextual factors have a consistent relationship to Disturbance Management Principles (DMPs). The product and SC environment characteristics are contextual factors that are hard to change and these characteristics initiate the use of specific DMPs as well as constrain the use of potential response actions. The process and the SC network characteristics are contextual factors that are easier to change, and they are affected by the use of the DMPs. We also found a notable relationship between the type of DMP likely to be used and the particular combination of contextual factors present in the observed SC.
To address RQ4, we presented a new method for vulnerability assessments, the VULA method. The VULA method helps to identify how much a company is underperforming on a specific Key Performance Indicator (KPI) in the case of a disturbance, how often this would happen and how long it would last. It ultimately informs the decision maker about whether process redesign is needed and what kind of redesign strategies should be used in order to increase the SC’s robustness. The VULA method is demonstrated in the context of a meat SC using discrete-event simulation. The case findings show that performance robustness can be assessed for any KPI using the VULA method.
To sum-up the project, all findings were incorporated within an integrated framework for designing robust SCs. The integrated framework consists of the following steps: 1) Description of the SC scenario and identification of its specific contextual factors; 2) Identification of disturbances that may affect KPIs; 3) Definition of the relevant KPIs and identification of the main disturbances through assessment of the SC performance robustness (i.e. application of the VULA method); 4) Identification of the sources of vulnerability that may (strongly) affect the robustness of performances and eventually increase the vulnerability of the SC; 5) Identification of appropriate preventive or disturbance impact reductive redesign strategies; 6) Alteration of SC scenario elements as required by the selected redesign strategies and repeat VULA method for KPIs, as defined in Step 3.
Contributions of this research are listed as follows. First, we have identified emerging research areas - SC robustness, and its counterpart, vulnerability. Second, we have developed a definition of SC robustness, operationalized it, and identified and structured the relevant elements for the design of robust SCs in the form of a research framework. With this research framework, we contribute to a better understanding of the concepts of vulnerability and robustness and related issues in food SCs. Third, we identified the relationship between contextual factors of food SCs and specific DMPs used to maintain robust SC performances: characteristics of the product and the SC environment influence the selection and use of DMPs; processes and SC networks are influenced by DMPs. Fourth, we developed specific metrics for vulnerability assessments, which serve as a basis of a VULA method. The VULA method investigates different measures of the variability of both the duration of impacts from disturbances and the fluctuations in their magnitude.
With this project, we also hope to have delivered practical insights into food SC vulnerability. First, the integrated framework for the design of robust SCs can be used to guide food companies in successful disturbance management. Second, empirical findings from case studies lead to the identification of changeable characteristics of SCs that can serve as a basis for assessing where to focus efforts to manage disturbances. Third, the VULA method can help top management to get more reliable information about the “health” of the company.
The two most important research opportunities are: First, there is a need to extend and validate our findings related to the research framework and contextual factors through further case studies related to other types of (food) products and other types of SCs. Second, there is a need to further develop and test the VULA method, e.g.: to use other indicators and statistical measures for disturbance detection and SC improvement; to define the most appropriate KPI to represent the robustness of a complete SC. We hope this thesis invites other researchers to pick up these challenges and help us further improve the robustness of (food) SCs.

Determinants of WTP for Prosecco wine: A latent class regression with attitudinal responses

Purpose – Under investigation is Prosecco wine, a sparkling white wine from North-East Italy.
Information collection on consumer perceptions is particularly relevant when developing market
strategies for wine, especially so when local production and certification of origin play an important
role in the wine market of a given district, as in the case at hand. Investigating and characterizing the
structure of preference heterogeneity become crucial steps in every successful marketing strategy. The
purpose of this paper is to investigate the sources of systematic differences in consumer preferences.
Design/methodology/approach – The paper explores the effect of inclusion of answers to
attitudinal questions in a latent class regression model of stated willingness to pay (WTP) for this
specialty wine. These additional variables were included in the membership equations to investigate
whether they could be of help in the identification of latent classes. The individual specific WTPs from
the sampled respondents were then derived from the best fitting model and examined for consistency.
Findings – The use of answers to attitudinal question in the latent class regression model is found to
improve model fit, thereby helping in the identification of latent classes. The best performing model
obtained makes use of both attitudinal scores and socio-economic covariates identifying five latent
classes. A reasonable pattern of differences in WTP for Prosecco between CDO and TGI types were
derived from this model.
Originality/value – The approach appears informative and promising: attitudes emerge as
important ancillary indicators of taste differences for specialty wines. This might be of interest per se
and of practical use in market segmentation. If future research shows that these variables can be of use
in other contexts, it is quite possible that more attitudinal questions will be routinely incorporated in
structural latent class hedonic models.

Lung clearance index: Evidence for use in clinical trials in cystic fibrosis

The ECFS-CTN Standardisation Committee has undertaken this review of lung clearance index as part of the group's work on evaluation of clinical endpoints with regard to their use in multicentre clinical trials in CF. The aims were 1) to review the literature on reliability, validity and responsiveness of LCI in patients with CF, 2) to gain consensus of the group on feasibility of LCI and 3) to gain consensus on answers to key questions regarding the promotion of LCI to surrogate endpoint status. It was concluded that LCI has an attractive feasibility and clinimetric properties profile and is particularly indicated for multicentre trials in young children with CF and patients with early or mild CF lung disease. This is the first article to collate the literature in this manner and support the use of LCI in clinical trials in CF.

A question of taste: Recognising the role of latent preferences and attitudes in analysing food choices

There has long been substantial interest in understanding consumer food choices, where a key complexity in this context is the potentially large amount of heterogeneity in tastes across individual consumers, as well as the role of underlying attitudes towards food and cooking. The present paper underlines that both tastes and attitudes are unobserved, and makes the case for a latent variable treatment of these components. Using empirical data collected in Northern Ireland as part of a wider study to elicit intra-household trade-offs between home-cooked meal options, we show how these latent sensitivities and attitudes drive both the choice behaviour as well as the answers to supplementary questions. We find significant heterogeneity across respondents in these underlying factors and show how incorporating them in our models leads to important insights into preferences. 

Law and Society: Volume I: Historical development

The thriving and well-established field of Law and Society (also referred to as Sociolegal Studies) has diverse methodological influences; it draws on social-scientific and arts-based methods. The approach of scholars researching and teaching in the field often crosses disciplinary borders, but, broadly speaking, Law and Society scholarship goes behind formalism to investigate how and why law operates, or does not operate as intended, in society. By exploring law’s connections with broader social and political forces—both domestic and international—scholars gain valuable perspectives on ideology, culture, identity, and social life. Law and Society scholarship considers both the law in contexts, as well as contexts in law.
Law and Society flourishes today, perhaps as never before. Academic thinkers toil both on the mundane and the local, as well as the global, making major advances in the ways in which we think both about law and society. Especially over the last four decades, scholarly output has rapidly burgeoned, and this new title from Routledge’s acclaimed Critical Concepts in Law series answers the need for an authoritative reference collection to help users make sense of the daunting quantity of serious research and thinking.
Edited by the leading scholars in the field, Law and Society brings together in four volumes the vital classic and contemporary contributions. Volume I is dedicated to historical antecedents and precursors. The second volume covers methodologies and crucial themes. The third volume assembles key works on legal processes and professional groups, while the final volume of the collection focuses on substantive areas. Together, the volumes provide a one-stop ‘mini library’ enabling all interested researchers, teachers, and students to explore the origins of this thriving subdiscipline, and to gain a thorough understanding of where it is today.

Law and Society: Volume II: Methodologies and themes

The thriving and well-established field of Law and Society (also referred to as Sociolegal Studies) has diverse methodological influences; it draws on social-scientific and arts-based methods. The approach of scholars researching and teaching in the field often crosses disciplinary borders, but, broadly speaking, Law and Society scholarship goes behind formalism to investigate how and why law operates, or does not operate as intended, in society. By exploring law’s connections with broader social and political forces—both domestic and international—scholars gain valuable perspectives on ideology, culture, identity, and social life. Law and Society scholarship considers both the law in contexts, as well as contexts in law.
Law and Society flourishes today, perhaps as never before. Academic thinkers toil both on the mundane and the local, as well as the global, making major advances in the ways in which we think both about law and society. Especially over the last four decades, scholarly output has rapidly burgeoned, and this new title from Routledge’s acclaimed Critical Concepts in Law series answers the need for an authoritative reference collection to help users make sense of the daunting quantity of serious research and thinking.
Edited by the leading scholars in the field, Law and Society brings together in four volumes the vital classic and contemporary contributions. Volume I is dedicated to historical antecedents and precursors. The second volume covers methodologies and crucial themes. The third volume assembles key works on legal processes and professional groups, while the final volume of the collection focuses on substantive areas. Together, the volumes provide a one-stop ‘mini library’ enabling all interested researchers, teachers, and students to explore the origins of this thriving sub discipline, and to gain a thorough understanding of where it is today.

Law and Society: Volume III: Legal Processes and Professional Groups within the Legal Field

The thriving and well-established field of Law and Society (also referred to as Socio-legal Studies) has diverse methodological influences; it draws on social-scientific and arts-based methods. The approach of scholars researching and teaching in the field often crosses disciplinary borders, but, broadly speaking, Law and Society scholarship goes behind formalism to investigate how and why law operates, or does not operate as intended, in society. By exploring law’s connections with broader social and political forces—both domestic and international—scholars gain valuable perspectives on ideology, culture, identity, and social life. Law and Society scholarship considers both the law in contexts, as well as contexts in law.
Law and Society flourishes today, perhaps as never before. Academic thinkers toil both on the mundane and the local, as well as the global, making major advances in the ways in which we think both about law and society. Especially over the last four decades, scholarly output has rapidly burgeoned, and this new title from Routledge’s acclaimed Critical Concepts in Law series answers the need for an authoritative reference collection to help users make sense of the daunting quantity of serious research and thinking.
Edited by the leading scholars in the field, Law and Society brings together in four volumes the vital classic and contemporary contributions. Volume I is dedicated to historical antecedents and precursors. The second volume covers methodologies and crucial themes. The third volume assembles key works on legal processes and professional groups, while the final volume of the collection focuses on substantive areas. Together, the volumes provide a one-stop ‘mini library’ enabling all interested researchers, teachers, and students to explore the origins of this thriving sub discipline, and to gain a thorough understanding of where it is today.