pairheatmap: Comparing expression profiles of gene groups in heatmaps

This paper presents a new visualization software called pairheatmap, which is able to generate and compare two heatmaps so as to compare expression patterns of gene groups. It adds a conditioning variable such as time to the heatmap, and provides separate clustering for row groups in the first heatmap in order to visualize pattern changes between two heatmaps. pairheatmap is developed in R statistical environment. It provides: (1) the flexible framework for comparing two heatmaps; and (2) high-quality figures based on R package grid. The general architecture can be efficiently incorporated into bioinformatics pipeline. The package and user documentation are free to download at http://cran.r-project.org/web/packages/pairheatmap/index.html.     

DISCRETE EVENT-DYNAMIC SYSTEMS FOR MODELING DYNAMIC VALUED NETS

The last few years have seen the development of Discrete Event-Dynamic Net Systems^1,2 as instruments for modeling complex systems. They are able to achieve the following objectives:

—formality of the modeling methodology

—ability to model static and dynamic aspects

—ability to pass between levels of differently rich structures by morphisms

—uniform representation of the communication process as

—an information process

—a decision process and

—a control process

—homogeneity of the representation and modeling methods

—ability to derive qualitative and quantitative statements.

The foundation is provided by a Discrete Event-Dynamic Net System which includes the axiomatic declaration of general Petri nets. In order to calculate the structural and dynamic aspects, so-called Petri net machines are developed. It is shown that this approach can even be used to treat the following aspects:

—use of time during the process

—increase of costs during the generation and transportation of information

—augmentation, evaluation and transformation of information objects.

Recursive formulas are derived and some examples calculated.     

The Observer-Generated Information Process: Composite Stages,Cooperative “Logical” Structure,and Self-Organization

Conventional information science generally considers an information process, but traditionally uses the probability measure for random events, and Shannon’s entropy measure as an uncertainty function of the states. The cutting process on separated states decreases quantity information concealed in the states correlation, holding hidden process information.

Up to now, “information process” has not had a scientifically conclusive definition nor its implicit structure.

The presenting information process performs logical operations with discrete information units (Bits) to achieve a goal, integrating the discrete mutually connected sequence of symbols and the extracting process’ hidden information in the structure of an information Observer. The probing time-space observation develops the unit of space-time geometry-memorizing logic.

The defined information process starts generating observations of a random process via the logic of probing impulses, sequentially cutting the process entropy measure and creating the discrete information units whose integration enfolds the information geometrical structure of an Observer. Found composite stages of the information process and the synthesized optimal process trajectory minimize observation time in an artificially designed information Observer with intellectual searching logic. The analytical modeling, computer simulations, and experimental applications validate the results.     

Vollvirtualisierung – Beitrag der Wirtschaftsinformatik zu einer Vision

Ohne Zusammenfassung This article is also available in English via http://www.springerlink.com and http://www.bise-journal.org: Buhl HU, Winter R (2008) Full Virtualization – BISE’s Contribution to a Vision. Bus Inf Syst Eng. doi: .     

A THEORETICAL STUDY ON ADAPTIVE QUALITY CONTROL SYSTEMS

This paper is a study of an adaptive quality control system from a viewpoint of quality goal. The main purpose is to introduce a conceptual framework for setting up quality goals which are in accordance with the external environment and internal capacity of quality control systems. We apply a mathematical general systems approach.

The results of our paper are summarized as follows:

1)As important decision-making in adaptive QCS, the decision-making for estimalion of fitness and examination of attainability are proposed and formalized mathematically.

2)A refinement process is formalized in which models are revised according to the changes of market.

3)Basic steps for setting quality goals are obtained which are based on the above formalization.     

The Proactive and Preventive Privacy (3P) Framework for IoT Privacy by Design

The Problem

Internet of Things (IoT) is providing new services and insights by sensing contextual data but there are growing concerns of privacy risks from users that need immediate attention.

The Reason

The IoT devices and smart services can capture Personally Identifiable Information (PII) without user knowledge or consent. The IoT technology has not reached the desired level of maturity to standardize security and privacy requirements.

The Solution

IoT Privacy by Design is a user-centric approach for enabling privacy with security and safety as a ‘win-win’ positive outcome of IoT offerings, irrespective of business domain. The Proactive and Preventive Privacy (3P) Framework proposed in this paper should be adopted by the IoT stakeholders for building trust and confidence in end users about IoT devices and smart services.     

THEORY OF CYBERNETIC AND INTELLIGENT MACHINE BASED ON LIE COMMUTATORS

Many attempts^{1, 7, 8, 35} have been made to overcome the limit imposed by the Turing Machine³⁴ to realise general mathematical functions and models of (physical) phenomena.

They center around the notion of computability.

In this paper we propose a new definition of computability which lays the foundations for a theory of cybernetic and intelligent machines in which the classical limits imposed by discrete algorithmic procedures are offset by the use of continuous operators on unlimited data. This data is supplied to the machine in a totally parallel mode, as a field or wave.

This theory of machines draws its concepts from category theory, Lie algebras, and general systems theory. It permits the incorporation of intelligent control into the design of the machine as a virtual element. The incorporated control can be realized in many (machine) configurations of which we give three:

a) a quantum mechanical realization appropriate to a possible understanding of the quantum computer and other models of the physical microworld,

b) a stochastic realization based on Kolmogorov-Gabor theory leading to a possible understanding of generalised models of the physical or thermodynamic macroworld, and lastly

c) a classical mechanical realization appropriate lo the study of a new class of robots.

Particular applications at a fundamental level are cited in geometry, mathematics, biology, acoustics, aeronautics, quantum mechanics, general relativity and. Markov chains. The proposed theory therefore opens a new way towards understanding the processes that underlie intelligence.     

Measuring and ranking attacks based on vulnerability analysis

As the number of software vulnerabilities increases, the research on software vulnerabilities becomes a focusing point in information security. A vulnerability could be exploited to attack the information asset with the weakness related to the vulnerability. However, multiple attacks may target one software product at the same time, and it is necessary to rank and prioritize those attacks in order to establish a better defense. This paper proposes a similarity measurement to compare and categorize vulnerabilities, and a set of security metrics to rank attacks based on vulnerability analysis. The vulnerability information is retrieved from a vulnerability management ontology integrating commonly used standards like CVE (http://www.cve.mitre.org/), CWE (http://www.cwe.mitre.org/), CVSS (http://www.first.org/cvss/), and CAPEC (http://www.capec.mitre.org/). This approach can be used in many areas of vulnerability management to secure information systems and e-business, such as vulnerability classification, mitigation and patching, threat detection and attack prevention.     

DEVELOPMENT OF AN AUTOMATIC OBJECT-ORIENTED CONTINUOUS SIMULATION ENVIRONMENT

The construction of automatic control and modelling environments has been attempted using shallow reasoning expert systems. The inadequacy of this approach for real-life systems has become apparent, and the need for deeper knowledge—which can only be obtained by extensive simulation—is now acknowledged.

The simulation process, which consists of model building and model selection, followed by the generation and execution of a software simulator, can be partially automated if an Object-Oriented methodology is adopted. In this article, a methodology is presented, which is presently under investigation in the DESiRE (Dynamic Expert Systems in Robotic Experimentation)project

In the modelling phase, a hierarchical, uniform way of describing and manipulating continuous and discrete models is needed, if the highly desirable reusability of submodels is to be achieved. This is only possible if a clear distinction is made between bare models (and information about their intrinsic coupling) and causal simulation experiment-related data.

In the simulation phase, before generating numerical simulation code, a symbolic reduction of the continuous parts of the model is performed, thus eliminating inaccuracy introduced by the untimely application of possibly unstable numerical algorithms.

Finally, from the reduced representation, executable simulator-objects are produced for use in a distributed environment.     

Normative data on the one-handed static pull strength of a Chinese population and a comparison with American data

We assess the one-handed static pull strength of a Chinese population and compare it to that of an American sample. Fifty men and 50 women in five age groups were asked to exert their maximum one-handed pull strength in three pulling directions (across, front and side) and from four pulling heights (61 cm, 76 cm, waist height and above-shoulder height). The results showed that women had less pull strength than men under all of the conditions tested. The front and side pulling resulted in the greatest pull strength, with a decrease detected when the pulling height was increased. The American sample exhibited greater strength than the Chinese. Body mass and men’s handgrip force were also associated with the pull strength. These variables should be taken into account in the development of tasks related to one-handed pulling.

Practitioner summary:

In this paper, we report a laboratory-based experiment conducted to assess the one-handed static pull strength of a Chinese population and compare the results with those of an American population. The variables associated with pull strength included gender, pulling direction, pulling height, race, body mass and men’s handgrip force.     

Forecasting Ranking in Harness Racing Using Probabilities Induced by Expected Positions

Ranked events are pivotal in many important AI-applications such as Question Answering and recommendations systems. This paper studies ranked events in the setting of harness racing.

For each horse there exists a probability distribution over its possible rankings. In the paper, it is shown that a set of expected positions (and more generally, higher moments) for the horses induces this probability distribution.

The main contribution of the paper is a method, which extracts this induced probability distribution from a set of expected positions. An algorithm is proposed where the extraction of the induced distribution is given by the estimated expectations. MATLAB code is provided for the methodology.

This approach gives freedom to model the horses in many different ways without the restrictions imposed by for instance logistic regression. To illustrate this point, we employ a neural network and ordinary ridge regression.

The method is applied to predicting the distribution of the finishing positions for horses in harness racing. It outperforms both multinomial logistic regression and the market odds.

The ease of use combined with fine results from the suggested approach constitutes a relevant addition to the increasingly important field of ranked events.     

Effects of age and body mass index on breast characteristics: a cluster analysis

Limited research has quantified variation in the characteristics of the breasts among women and determined how these breast characteristics are influenced by age and body mass. The aim of this study was to classify the breasts of women in the community into different categories based on comprehensive and objective measurements of the characteristics of their breasts and torsos, and to determine the effect of age and body mass index on the prevalence of these breast categories. Four breast characteristic clusters were identified (X-Large, Very-ptotic & Splayed; Large, Ptotic & Splayed; Medium & Mildly-ptotic; and Small & Non-ptotic), with age and BMI shown to significantly affect the breast characteristic clusters. These results highlight the difference in breast characteristics exhibited among women and how these clusters are affected by age and BMI. The breast characteristic clusters identified in this study could be used as a basis for future bra designs and sizing systems in order to improve bra fit for women.

Practitioner summary: This original research provides evidence for bra designers and manufacturers on the diverse breast characteristics exhibited by women within the population and the significant effect that both body mass index and age have on the breast characteristic clusters. Future bra designs should consider the variation in breast characteristics among women.

Abbreviations: BMI: Body Mass Index; UBCC: Under-bust chest circumference     

The impact of external facial features on the construction of facial composites

Witnesses may construct a composite face of a perpetrator using a computerised interface. Police practitioners guide witnesses through this unusual process, the goal being to produce an identifiable image. However, any changes a perpetrator makes to their external facial-features may interfere with this process. In Experiment 1, participants constructed a composite using a holistic interface one day after target encoding. Target faces were unaltered, or had altered external-features: (i) changed hair, (ii) external-features removed or (iii) naturally-concealed external-features (hair, ears, face-shape occluded by a hooded top). These manipulations produced composites with more error-prone internal-features: participants’ familiar with a target’s unaltered appearance less often provided a correct name. Experiment 2 applied external-feature alterations to composites of unaltered targets; although whole-face composites contained less error-prone internal-features, identification was impaired. Experiment 3 replicated negative effects of changing target hair on construction and tested a practical solution: selectively concealing hair and eyes improved identification.

Practitioner Summary: The research indicates that when a target identity disguises or changes hair, this can lead to a witness (or victim) constructing a composite that is less readily identified. We assess a practical method to overcome this forensic issue.

Abbreviation: GEE: Generalized Estimating Equations     

Role network measures to assess healthcare team adaptation to complex situations: the case of venous thromboembolism prophylaxis

Hospitals are complex environments that rely on clinicians working together to provide appropriate care to patients. These clinical teams adapt their interactions to meet changing situational needs. Venous thromboembolism (VTE) prophylaxis is a complex process that occurs throughout a patient’s hospitalisation, presenting five stages with different levels of complexity: admission, interruption, re-initiation, initiation, and transfer. The objective of our study is to understand how the VTE prophylaxis team adapts as the complexity in the process changes; we do this by using social network analysis (SNA) measures. We interviewed 45 clinicians representing 9 different cases, creating 43 role networks. The role networks were analysed using SNA measures to understand team changes between low and high complexity stages. When comparing low and high complexity stages, we found two team adaptation mechanisms: (1) relative increase in the number of people, team activities, and interactions within the team, or (2) relative increase in discussion among the team, reflected by an increase in reciprocity.

 

Practitioner Summary: The reason for this study was to quantify team adaptation to complexity in a process using social network analysis (SNA). The VTE prophylaxis team adapted to complexity by two different mechanisms, by increasing the roles, activities, and interactions among the team or by increasing the two-way communication and discussion throughout the team. We demonstrated the ability for SNA to identify adaptation within a team.     

The Importance of Auditing Your Company’s Strategic Plan

A company’s strategic plan is its long-term outlook that sets out the plans, goals, objectives and actions for the next three to ten years. The board needs an objective assurance that the plan was properly developed. The internal audit function is best positioned to provide this assurance. The reason: it is one of the board’s most powerful mechanisms for understanding the full spectrum of key governance, risk, and control issues facing the company embodied in the strategic plan.

Auditing a strategic plan begins with a review of what it constitutes (its elements) and the methodology (its process) used in developing the plan. It thus becomes much easier to focus the audit effort in determining whether the output for each step along the way in these two broad streams has been achieved.

If not carefully planned and executed, a strategic plan audit could do irreparable damage to the reputation of the audit effort throughout the organization. As a result, it requires a multi-talented team with a high-powered leader, preferably the chief audit executive.

Although a strategic plan fails due to such common factors as planning teams lacking an understanding of the business, lack of commitment, not having the right people, or not adapting to a changing environment to take full advantage of technological developments, there is a key reason often overlooked: lack of an audit of the plan itself which, if done properly, could uncover these reasons for failure long before they happen.     

Home is where the head is: a distributed cognition account of personal health information management in the home among those with chronic illness

Managing chronic illness requires personal health information management (PHIM) to be performed by lay individuals. Paramount to understanding the PHIM process is understanding the sociotechnical system in which it frequently occurs: the home environment. We combined distributed cognition theory and the patient work system model to investigate how characteristics of the home interact with the cognitive work of PHIM. We used a 3D virtual reality CAVE that enabled participants who had been diagnosed with diabetes (N = 20) to describe how they would perform PHIM in the home context. We found that PHIM is distinctly cognitive work, and rarely performed ‘in the head’. Rather, features of the physical environment, tasks, people, and tools and technologies present, continuously shape and are shaped by the PHIM process. We suggest that approaches in which the individual (sans context) is considered the relevant unit of analysis overlook the pivotal role of the environment in shaping PHIM.

Practitioner Summary:

We examined how Personal Health Information Management (PHIM) is performed in the homes of diabetic patients. We found that approaches to studying cognition that focus on the individual, to the exclusion of their context, overlook the pivotal role of environmental, social, and technological features in shaping PHIM.     

The process evaluation of two alternative participatory ergonomics intervention strategies for construction companies

To gain insight into the process of applying two guidance strategies – face-to-face (F2F) or e-guidance strategy (EC) – of a Participatory Ergonomics (PE) intervention and whether differences between these guidance strategies occur, 12 construction companies were randomly assigned to a strategy. The process evaluation contained reach, dose delivered, dose received, precision, competence, satisfaction and behavioural change of individual workers. Data were assessed by logbooks, and questionnaires and interviews at baseline and/or after six months. Reach was low (1%). Dose delivered (F2F: 63%; EC: 44%), received (F2F: 42%; EC: 16%) were not sufficient. The precision and competence were sufficient for both strategies and satisfaction was strongly affected by dose received. For behavioural change, knowledge (F2F) and culture (EC) changed positively within companies. Neither strategy was delivered as intended. Compliance to the intervention was low, especially for EC. Starting with a face-to-face meeting might lead to higher compliance, especially in the EC group.

Practitioner Summary: This study showed that compliance to a face-to-face and an e-guidance strategy is low. To improve the compliance, it is advised to start with a face-to-face meeting to see which parts of the intervention are needed and which guidance strategy can be used for these parts.

Trial registration: ISRCTN73075751     

A comfort assessment of existing cervical orthoses

Purpose: Identify location and intensity of discomfort experienced by healthy participants wearing cervical orthoses.

Method: Convenience sample of 34 healthy participants wore Stro II, Philadelphia, Headmaster, and AspenVista^® cervical orthoses for four-hour periods. Participants reported discomfort level (scale 0–6) and location.

Results: Participants reported mean discomfort for all orthoses over the four-hour test between ‘a little discomfort’ and ‘very uncomfortable’ (mean discomfort score = 1.64, SD = 1.50). Seven participants prematurely stopped tests due to pain and six reported maximum discomfort scores. Significant linear increase in discomfort with duration of wear was found for all orthoses. Significantly less discomfort was reported with Stro II than Headmaster and Philadelphia. Age correlated with greater perceived discomfort. Orthoses differed in the location discomfort was experienced.

Conclusion: Existing cervical orthoses cause discomfort influenced by design and duration of wear with orthoses’ design the more significant factor. This work informed the design of a new orthosis and future orthoses developments.

Practitioner Summary: The purpose of this study was to gain greater knowledge about the discomfort caused by wearing of existing neck orthoses in order to inform the design and development of a new neck orthosis. This study gathers empirical data from a surrogate population and concludes that orthosis design is more influential than the duration of wear.     

Book reviews

Computer Software: legal protection in the United Kingdom Henry Carr & Richard Arnold, 1992 London: Sweet & Maxwell, 2nd ed, xv + 312 pp., £45.00 (hardback)

Advanced Information Systems for Lawyers V. Mital & L. Johnson, 1992 London: Chapman & Hall. pp. 306, £35.00

Law of Contract Laurence Koffman & Elizabeth MacDonald, 1992 London: Fourmat Publishing, 430 pp., paperback £22.50

The Electronic Media and the Transformation of Law M. Ethan Katsh, 1991 Oxford: Oxford University Press. £13.95