bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiology of depression and distress in patients with inflammatory bowel disease (IBD) and validation of an indicator scale of perceived stress for psychosocial impairments
Authors: Hardt J. , Conrad S. , Muche-Borowski C. , Raspe H.
Published: May 2011

Background

Previous studies showed associations of stress and episodes of active disease [1,2]. We reported survey data on psychosocial problems of IBD patients [3]. This study investigates associations of stress with health impairments and analyses a scale of perceived stress as an indicator for psychosocial impairments (construct/criterion validity) [4].

Methods

In a multiregional German survey in 2005, 1083 patients with Crohn's disease (CD) and ulcerative colitis were recruited (gastroenterological practices, university outpatient clinics, patient organization). The questionnaire incorporated WHO's ICF [5] and established items and scales (i.a. HADS [6]). Scale construction followed item response theory analysing psychometric properties.

Results

Of the survey responders (58% CD, 65% female, mean age 42yrs), ⅓ reported severe fatigue. Clinically relevant anxiety was observed in 24%, depression in 29% of men and 21% of women. With three items we constructed a scale with good psychometric properties. Three groups (low, moderate, high perceived stress) were identified, differing substantially in reported anxiety/depression and the GIBDI disease activity score.

Conclusions

IBD patients report multiple psychosocial impairments. The scale of perceived stress may identify IBD patients with high demand for psychosocial attendance, if confirmed in independent samples. For enhanced secondary prevention [7] we propose integration of this psychosocial indicator into the diagnostic process.
The role of psychological distress, somatization and personality traits in the formation of IBD patients' health-related quality of life (HRQOL) and smoking habits
Authors: Hyphantis T.
Published: May 2011

Introduction

Clinical parameters predict HRQoL in inflammatory bowel disease (IBD), however some patients have impaired HRQoL despite clinical remission; furthermore, Crohn's disease (CD) is associated with smoking, while ulcerative colitis (UC) is largely a nonsmokers’ disease, indicating that psychological distress and personality variables might mediate the relationship of clinical variables with HRQoL and smoking.

Aims

To assess psychological distress and personality traits in IBD and their contribution to the formation of HRQoL and smoking habits.

Methods

In 76 IBD outpatients we compared psychological distress symptoms and defensive profile between CD and UC. In another study of 185 IBD patients, we tested the relation of psychological distress, defense mechanisms and personality traits with HRQoL, smoking, and nicotine dependence.

Results

CD patients presented a more immature defensive profile. The more psychologically mature IBD patients had lower relapses and surgical operations’ rates. Psychological distress was associated with impaired HRQoL in a dose-response fashion. Somatization was independently associated with impaired HRQoL and mediated the relationships of anxiety and depression with HRQoL. In CD, the relationship of the smoking-linked personality characteristic “impulsive sensation seeking” with current smoking and nicotine dependence was stronger.

Conclusions

IBD patients exhibit several specific psychological difficulties in adaptation to stressors. Apart from addressing timely psychological distress and somatization symptoms, clinicians and consultation-liaison psychiatrists should consider the patients’ defensive profile, since such personality traits, although usually underestimated, are strongly independently associated with the disease's outcome. Our findings might be also relevant to more effective interventions targeting smoking cessation in CD patients.
Associations of affective disorder in patients with inflammatory bowel disease
Authors: Baig B.J. , Lees C.W. , Johnstone E.C. , James V. , Satsangi J. , Lawrie S.M.
Published: May 2011

Introduction

Inflammatory Bowel Disease (IBD) is associated with co morbid depression and anxiety of up to 42%. Corticosteroids, used commonly in IBD, are known to cause psychiatric side-effects and could be an independent risk factor for affective illness. Recent studies show that depression is also associated with raised CRP and IL6.

Aims

This study aims to show which demographic, clinical, medication and immunological factors are predictors of anxiety and depression in IBD.

Methods

The IBD, Steroids and Affective Disorder (ISA) study is a cross-sectional study of IBD patients in Edinburgh, UK. Out patients underwent assessment including Hospital Anxiety Depression Scale (HADS) past psychiatric history, steroid medication history, inflammatory markers, the Medication Adherence Rating Scale (MARS) and Altman Self Rated Mania Scale (ARSM).

Results

326 patients with Crohns and 256 with Colitis (72% of clinic attendees) were recruited. 251 (43%) patients scored 12 or above on the HADS questionnaire. 45% of patients had previously suffered from affective illness. Patients on Prednisolone and Budesonide scored significantly higher on HADS Depression (p = 0.03 and p = 0.002) as did those who had been on Prednisolone for more than 8 weeks (p = 0.041). Being on prednisolone was not associated with increased Colitis and Crohns activity indices (p = 0.2). HADS scores were measured against other disease and demographic variables.

Conclusion

Affective illness is common in the IBD population and the prescription and duration of systemic corticosteroids are associated with depression. Biological and disease variables may play an important role in co morbid affective illness in IBD
Socioeconomic and psychological factors associated with non-adherence to treatment in IBD patients: Results of the isseo survey
Authors: Nahon S.
Published: May 2011

Introduction

Treatment is a key condition in preventing relapses in inflammatory bowel disease. The aims of the ISSEO study were specifically to study socioeconomic and psychological factors and adherence to treatment in a large cohort of IBD patients.

Methods

A questionnaire concerning demographic, clinical and psychosocial characteristics was mailed to 6000 IBD patients belonging to the French association of IBD patients (AFA). The questionnaire was also available on the website of the AFA for non-member patients to answer. Good adherence to treatment was defined as taking ≥80% of prescribed medication. Socioeconomic deprivation was assessed using the specific EPICES score (http://www.cetaf.asso.fr) developed in France. Anxiety and depression were assessed using the HAD scale.

Results

1069 women and 594 men (43.6 ± 15.4 yrs) completed the questionnaire, 1450 (87%) of them belonged to the AFA. 1044 had Crohn's disease, 36 indeterminate colitis and 583 ulcerative colitis. Adherence ≥80% was reported by 90% of patients. Logistic regression identified the following factors for good adherence: anti-TNF alpha therapy (OR 2.3, 95% CI 1.46–3.63) and membership of the AFA (OR 1.67, 95% CI 1.05–2.64), while anxiety (OR 0.62, 95% CI 0.42–0.90), and constraints related to treatment (OR 0.32, 95% CI 0.23–0.47) were associated with non-adherence.

Conclusion

In this large cohort of IBD patients, psychological distress and constraints related to treatment decrease adherence to treatment, while membership of a patients’ association improves it.
Molecular systems biology and management of complex data sets
Authors: Gebicke-Haerter P.
Published: May 2011

Theoretically, high throughput technologies that have become available in molecular biology and are continuously refined to generate even more reliable datasets permit more and more insights into ongoing dynamic events that may result in improvements of biological systems or the development of diseases. The more comprehensive datasets are the more they reflect the status of a molecular system. If they are obtained at various time points, they encompass its development. In practice, however, their biological interpretation remains a challenge. Presently, we do not have the tools required to decode the full biological message encrypted in e.g. expression profiling, genome-wide DNA-methylation patterns or in the so-called “histone code”. Consequently, strategies are aimed at picking molecular subnetworks that we are familiar with from previous work. Alternatively, unbiased approaches use as many data as possible for insertion into mathematical programs to perform time-dependent computer simulations of increasingly larger networks. Although this strategy appears to be straightforward and very attractive, its mandatory extension to large molecular networks presently reveals a lack of efficient mathematical tools and computational power. Advantages and shortcomings of available algorithms will be discussed.
Methodology of mapping in integrative molecular biology
Authors: Iris F.
Published: May 2011

Psychiatric illnesses remain of unclear etiopathogenesis and a variety of them can coexist, partly mimicking each other while contributing to and distorting symptomatic expressions. To understand the processes involved, it is necessary to unravel signalling pathways, complex interaction networks and metabolic alterations involving a plethora of anatomical components. Hence, whatever the nature of the alterations convincingly detected, these must be associated with their most-likely cellular contexts to then have a chance to reverse engineer the events that could have given rise to the observed alterations and predict their most plausible functional consequences. This requires the utilisation of analytical approaches collectively known as “Systems Biology”.

Systems biology explores how parts of biological entities function and interact to give rise to the behaviour of the system as a whole. But having said that, what can we actually do?

Two broad approaches to systems biology currently exist: the frequently followed mathematical (Bayesian) procedures and the more rarely encountered heuristic approaches.

Heuristic modelling plays the role of an architect (defines the nature, the structure, the functionalities and the contextual constrains of a process) while mathematical modelling plays the role of an engineer (reveals the dynamics and robustness of this process while defining the set of parameters sufficient to give rise to similar or very different phenotypes).

This talk will explain, through concrete examples, the approaches whereby one can harness heuristic frameworks to produce multi-level models of complex neurobiological processes that can then be independently tested and biologically validated or refuted.
Mesoscopic brain dynamics and mental disorders
Authors: Liljenström H.
Published: May 2011

Mesoscopic brain dynamics, typically studied with electro- and magnetoencephalography (EEG and MEG), display a rich complexity of oscillatory and chaotic-like states, including many different frequencies, amplitudes and phases. Presumably, these different dynamical states correspond to different mental states and functions, and studying transitions between such states could provide valuable insights into brain-mind relations that should also be of clinical interest. We use computational methods to investigate these transitions, with the objective of finding relations between structure, dynamics, and function. In particular, we have developed models of paleo- and neocortical structures, in order to study their mesoscopic neurodynamics, as a link between the microscopic neuronal and macroscopic mental events and processes. I will describe several types of models that emphasize network connectivity and structure, but which also include molecular and cellular properties at varying detail, depending on the particular problem and experimental data available. We use these models to study how phase transitions can be induced in the mesoscopic neurodynamics of cortical networks by internal (natural) and external (artificial) factors. I will discuss the models, and relate the simulation results to macroscopic phenomena, such as arousal, attention, anaesthesia, learning, and certain mental disorders.
Cultural competence in clinical practice
Authors: Bhugra D.
Published: May 2011

With increasing globalisation it is inevitable that along with goods, people will move too. Certain psychiatric disorders are more common among some groups of migrants. It is inevitable that there may be a degree of mismatch between the cultural values and beliefs of patients in comparison with their psychiatrists. Every individual has certain cultural values and it is vital that mental health professionals are not only aware of these values but are also conscious of their own values, prejudices and both strengths and cultural weaknesses. Cultural competence is at the core of good clinical practice. Skills and knowledge about other cultures can be learnt and clinicians also need to be aware of potential sources of conflict and sources from where they can gather information and then utilise it appropriately.
Transcultural telepsychiatry and its impact on patient satisfaction
Authors: Mucic D.
Published: May 2011

Introduction

National and International telepsychiatry service was established between Denmark and Sweden in order to increase access to cross-cultural expertise. Patient acceptability study was conducted to assess the patients’ attitudes toward the quality, advantages and disadvantages of telepsychiatry service.

Methods

Over a period January 2005-December 2007, 61 patients were treated via telepsychiatry by clinicians that speak patientsrespective mother tongues. Video-conferencing equipment connected the Little Prince Psychiatric Centre in Copenhagen with two hospitals, one asylum seekers’ centre and one social institution in Denmark. These stations were also connected to the Swedish department of the Centre. Number of languages spoken was 9 while the number of nationalities treated was 11. No interpreter assistance has been used.

After the end of the telepsychiatry contact all patients were asked to complete a satisfaction questionnaire.

Results

Patients reported a high level of acceptance and satisfaction with telepsychiatry. They expressed a wish to use telepsychiatry via their mother tongue, rather than interpreter-assisted mental health care in the future.

Discussion

The restricted physical contact and non-verbal communication of telepsychiatry was compensated by the fact that the doctor and patient spoke the same language and had similar cultural and/or national references. The results of the survey may contribute to further development of, primarily, European Telepsychiatry Network. However, this model may be used for conducting of larger international telepsychiatry service capable to provide mental health care toward diversity of patient populations underserved on their mother tongue worldwide.
Culturally competent mental health care
Authors: van Loon P.J.
Published: May 2011

A dynamic view of culture defines it as the semiotic system that people use to interpret their inner and outer worlds and that shapes their responses to it.

Culture is more than the fixed patterns of behaviour acquired and transmitted through symbols and related to a particular cultural group.

Cross cultural psychiatry makes use of both universalistic and relativistic concepts.

It is important to make use of these concepts as clinician in the diagnostic and therapeutic process with patients.

Attention will be paid to the concept of idioms of distress, how does the patient elaborate his suffering?

Clearly elucidation of the idioms of distress is essential in formulating an accurate diagnosis.

Another factor as emphasised in the Cultural Formulation which is highly relevant to this subject is the therapist patient relationship. Transference and countertransference issues related to the necessity of reconciling the meaning of verbal and nonverbal expressions of the patient along with contextual information about the patient and his environment with diagnostic critieria are relevant here.

Some research particularly related to how symptoms are expressed and carried out in the department in Rotterdam will be discussed in this workshop.
Culturally competence care of moroccan migrants
Authors: Moussaoui D.
Published: May 2011

About 15% of all Moroccans live abroad (4 and a half million), mostly in Europe and North America. For historic reasons, migration of Moroccans went essentially to France, Belgium, Holland, and more recently to Spain. Many of these migrants are well integrated, but many others do suffer from social bad integration. Those with mental disorders are probably those who are most at risk of non-integration.

Mental health workers are not always aware of the cultural background of the Moroccan migrant, including family structure and interactions, religious and traditional beliefs. In France and Holland, and recently in Spain, a few teams are highly interested in transcultural psychiatry and provide care to the migrants and teaching to other mental health professionals. Their number and resources are however far from being sufficient to cover all the field in the entire country. One of the solutions is to develop a teaching program for post-graduates in psychiatry on "Cultural sensitivity" in all departments of psychiatry. A collaboration between mental health workers from the North and the South of the Mediterranean Sea is highly desirable in this respect. This is why the Euro-Med Network on Migration and Mental Health was created in 2007.
The History and Organization of the European Federation of Psychologists’ Associations (EFPA)
Authors: Freeman Richard P. J. , Steyaert Sabine
Published: May 2011

In 1981, the European Federation of Professional Psychologists’ Associations (EFPPA) was formed with 13 member associations (one per country) and no centralized administrative support. Thirty years later, EFPPA has become EFPA with 35 member associations representing about 300,000 psychologists across Europe. EFPA is now based in offices in the center of Brussels, the administrative heart of Europe, with a Director and staff who support the work of the EFPA Executive Council and the various Standing Committees, Task Forces, and Working Groups. In this article, the development of EFPA and the challenges faced, and mostly overcome, are outlined.
The European Federation of Psychology Students’ Associations
Authors: Polišenská Veronika A.
Published: May 2011

This article describes the development of the European Federation of Psychology Students’ Associations (EFPSA) since its formation in 1987 up to 2011. It concentrates on the history of the organization and its structure and how it has changed over the years to accommodate the growing number of students, countries, and projects involved. It introduces the ideal of the “EFPSA spirit,” which is the experience of multiculturalism of the people and the friendships formed at various events. The article concludes with a view of the future of EFPSA.
EuroPsy: The Development of Standards for High-Quality Professional Education in Psychology
Authors: Lunt Ingrid
Published: May 2011

The paper presents a brief history of the EuroPsy initiative which began in 1998 and is now in the process of implementation across European countries in the European Federation of Psychologists’ Associations (EFPA). EuroPsy defines a standard of professional education that aims to promote a high quality of education and professional practice for psychologists. The initiative was substantially supported by developments within the European Union (EU) and more widely in Europe, in particular the so-called Bologna process. This process, however, had a major political focus with an explicit commitment to facilitate mobility. Concerns for quality and a high level of professional education and an implied focus on consumer or client protection may not always sit easily with a commitment to facilitating professional mobility. This paper presents some of the challenges and potential tensions inherent in the EuroPsy.
Psychology as a Profession and a Science
Authors: Poortinga Ype H. , Lunt Ingrid
Published: May 2011

The European Association of Psychologists’ Associations (EFPA) was created in 1981 as the European Association of Professional Psychologists’ Associations (EFPPA). We show that Shakespeare’s dictum “What’s in a name?” does not apply here and that the loss of the “first P” (the adjectival “professional”) was resisted for almost two decades and experienced by many as a serious loss. We recount some of the deliberations preceding the change and place these in a broader historical context by drawing parallels with similar developments elsewhere. Much of the argument will refer to an underlying controversy between psychology as a science and the practice of psychology, a controversy that is stronger than in most other sciences, but nevertheless needs to be resolved.
Transnational Ethical Guidance and the Development of the EFPA Meta-Code of Ethics
Authors: Lindsay Geoff
Published: May 2011

Ethical practice is one of the fundamental characteristics of a profession. The development of common codes was an early aim of the European Federation of Professional Psychologists Associations (EFPPA), now the European Federation of Psychologists Associations (EFPA), which sought to develop common standards across Member Associations. This paper describes: the development of the Meta-Code of Ethics, approved in 1995; the subsequent review of its fitness for purpose, leading to the second edition in 2005; and other guidance on ethical practice, including procedures for the evaluation of alleged unethical practice and for determining corrective actions to be taken, including mediation. The success of the Meta-code is reviewed, including its contribution to current initiatives to develop universal ethical practice by psychologists, in the context of new challenges arising from developments within psychology and from changes within society, including concerns about national security.
The Development of Psychotherapy as a Specialism for Psychologists
Authors: Lane David A. , Althaus Katharina
Published: May 2011

The development of psychotherapy as an area of expertise for psychologists has occupied the European Federation of Psychologists’ Associations (EFPA) for many years. Differences in regulations and practice within Europe, as well as the absence of the discipline as an area of practice in some countries, have complicated the establishment of European standards. This paper describes the efforts of the EFPA Task Force, later Standing Committee, on Psychotherapy to establish a standard. The problems faced included differing traditions and the existence of other nonpsychologists within the field of practice. In addition, debates over the development of a basic standard for European psychology delayed implementation of the specialist standards. The eventual resolution included three routes to recognition: a national register accepted by EFPA; a national training program similarly recognized; or a process by which individual psychologists presented their credentials to the national committee for acceptance. In each case the national committees had to seek endorsement from the EFPA European Awarding Committee to approve the nationally adopted process as meeting the EFPA standards. The establishment of these EFPA standards has enabled national associations to use the standards as a basis for discussion with their own regulatory authorities as well as in discussion with other bodies operating in this area of practice.
EFPA and Work on Disaster, Crisis, and Trauma Psychology
Authors: Saari Salli , Nuray Karanci A. , Yule William ,   EFPA Standing Committee on Disaster, Crisis, and Trauma Psychology
Published: May 2011

In response to increasing concern about the effects of crises, disaster, trauma and, more recently, terrorism, EFPA established first a working party and then a Standing Committee to advise on the part psychology can play in preparing for emergencies and responding to them. The Committee has drawn together evidence and views from across Europe and the wider international scene. It has worked closely with the European Commission and has embarked on further training for members from recently acceded countries. It has recommended better ways of liaising across countries so that in the event of cross-border incidents, more efficient and effective responses can be assured. In turn this has implications for the training of psychologists and other professionals involved in emergency planning and response. Currently, there is a move to develop quality standards for such training.
Contributions of the EFPA Standing Committee on Tests and Testing to Standards and Good Practice
Authors: Bartram Dave
Published: May 2011

The EFPA Standing Committee on Tests and Testing (SCTT) has been active in the development of standards relating to tests and test use in Europe for more than a decade. This paper summarizes the work of the SCTT with a particular focus on the development of its Test Review Model and its standards for test use. The latter are now being developed as the basis for a special post-EuroPsy qualification. The SCTT members have also been involved in the developments of the ISO 10667 and through this we have seen how members of the profession can have a major influence on standards that are designed for the wider community of assessors and test users rather than just focused on the needs of psychologists. EFPA needs to take an outward-looking approach if it is to cover all the ways in which psychology has an influence on society.
Sensitivity, robustness, and identifiability in stochastic chemical kinetics models
Authors: Komorowski Michał , Costa Maria J. , Rand David A. , Stumpf Michael P. H.
Published: May 2011

We present a novel and simple method to numerically calculate Fisher information matrices for stochastic chemical kinetics models. The linear noise approximation is used to derive model equations and a likelihood function that leads to an efficient computational algorithm. Our approach reduces the problem of calculating the Fisher information matrix to solving a set of ordinary differential equations. This is the first method to compute Fisher information for stochastic chemical kinetics models without the need for Monte Carlo simulations. This methodology is then used to study sensitivity, robustness, and parameter identifiability in stochastic chemical kinetics models. We show that significant differences exist between stochastic and deterministic models as well as between stochastic models with time-series and time-point measurements. We demonstrate that these discrepancies arise from the variability in molecule numbers, correlations between species, and temporal correlations and show how this approach can be used in the analysis and design of experiments probing stochastic processes at the cellular level. The algorithm has been implemented as a Matlab package and is available from the authors upon request.
End-binding proteins EB3 and EB1 link microtubules to ankyrin G in the axon initial segment
Authors: Leterrier Christophe , Vacher Hélène , Fache Marie-Pierre , d'Ortoli Stéphanie Angles , Castets Francis , Autillo-Touati Amapola , Dargent Bénédicte
Published: May 2011

The axon initial segment (AIS) plays a key role in maintaining the molecular and functional polarity of the neuron. The relationship between the AIS architecture and the microtubules (MTs) supporting axonal transport is unknown. Here we provide evidence that the MT plus-end-binding (EB) proteins EB1 and EB3 have a role in the AIS in addition to their MT plus-end tracking protein behavior in other neuronal compartments. In mature neurons, EB3 is concentrated and stabilized in the AIS. We identified a direct interaction between EB3/EB1 and the AIS scaffold protein ankyrin G (ankG). In addition, EB3 and EB1 participate in AIS maintenance, and AIS disassembly through ankG knockdown leads to cell-wide up-regulation of EB3 and EB1 comets. Thus, EB3 and EB1 coordinate a molecular and functional interplay between ankG and the AIS MTs that supports the central role of ankG in the maintenance of neuronal polarity.
Fast propagation of weakly pinned domain walls and current-assisted magnetization reversal in He+-irradiated Pt/Co/Pt nanotracks
Authors: Cormier M , Mougin A , Ferré J , Jamet J-P , Weil R , Fassbender J , Baltz V , Rodmacq B
Published: May 2011

Magnetic-domain-wall propagation is experimentally studied in nanotracks etched in ultrathin Pt/Co/Pt films with out-of-plane magnetic anisotropy, where pinning has been artificially reduced by low-dose He+-irradiation. Fast domain-wall propagation is demonstrated in such tracks under low magnetic fields, not greater than the fields necessary to make a domain wall propagate in the He+-irradiated plain films before patterning. A strong further enhancement of the track-magnetization reversal speed is obtained thanks to a Joule-heating-induced thermomagnetic effect, by applying magnetic-field and electrical-current pulses simultaneously to the track.
Ferrimagnetism and disorder of epitaxial Mn2−xCoxVAl Heusler compound thin films
Authors: Meinert Markus , Schmalhorst Jan-Michael , Reiss Günter , Arenholz Elke
Published: May 2011

The quaternary full Heusler compound Mn2−x
Co
x
VAl with x = 1 is predicted to be a half-metallic antiferromagnet. Thin films of the quaternary compounds with x = 0–2 were prepared by dc and RF magnetron co-sputtering on heated MgO (0 0 1) substrates. The magnetic structure was examined by x-ray magnetic circular dichroism and the chemical disorder was characterized by x-ray diffraction. Ferrimagnetic coupling of V to Mn was observed for Mn2VAl (x = 0). For x = 0.5, we also found ferrimagnetic order with V and Co antiparallel to Mn. The observed reduced magnetic moments are interpreted with the help of band structure calculations in the coherent potential approximation. Mn2VAl is very sensitive to disorder involving Mn, because nearest-neighbour Mn atoms couple antiferromagnetically. Co2VAl has B2 order and has reduced magnetization. In the cases with x ⩾ 0.9 conventional ferromagnetism was observed, closely related to the atomic disorder in these compounds.
Numerical analysis of the heat source characteristics of a two-electrode TIG arc
Authors: Ogino Y , Hirata Y , Nomura K
Published: May 2011

Various kinds of multi-electrode welding processes are used to ensure high productivity in industrial fields such as shipbuilding, automotive manufacturing and pipe fabrication. However, it is difficult to obtain the optimum welding conditions for a specific product, because there are many operating parameters, and because welding phenomena are very complicated. In the present research, the heat source characteristics of a two-electrode TIG arc were numerically investigated using a 3D arc plasma model with a focus on the distance between the two electrodes. The arc plasma shape changed significantly, depending on the electrode spacing. The heat source characteristics, such as the heat input density and the arc pressure distribution, changed significantly when the electrode separation was varied. The maximum arc pressure of the two-electrode TIG arc was much lower than that of a single-electrode TIG. However, the total heat input of the two-electrode TIG arc was nearly constant and was independent of the electrode spacing. These heat source characteristics of the two-electrode TIG arc are useful for controlling the heat input distribution at a low arc pressure. Therefore, these results indicate the possibility of a heat source based on a two-electrode TIG arc that is capable of high heat input at low pressures.
Thermally induced atomic diffusion at the interface between release agent coating and mould substrate in a glass moulding press
Authors: Masuda Jun , Yan Jiwang , Zhou Tianfeng , Kuriyagawa Tsunemoto , Fukase Yasushi
Published: May 2011

In a glass moulding press (GMP) for refractive/diffractive hybrid lenses, to improve the service life of nickel–phosphorus (Ni–P) plated moulds, it is necessary to control the diffusion of constituent elements from the mould into the release agent coating. In this study, diffusion phenomena of constituents of Ni–P plating are investigated for two types of release agent coatings, iridium–platinum (Ir–Pt) and iridium–rhenium (Ir–Re), by cross-sectional observation, compositional analysis and stress measurements. The results show that Ni atoms in the plating layer flow from regions of compressive stress to regions of tensile stress. In the case of the Ir–Pt coated mould, the diffusion of Ni is promoted from the grain boundaries between the Ni and Ni3P phases in the plating towards the surface of the Ir–Pt coating. However, in the Ir–Re coated mould, the diffusion of Ni is suppressed because the diffusion coefficient of Ni in the Ir–Re alloy is smaller than that in the Ir–Pt alloy, although the stress state is similar in both cases. By controlling the diffusion of Ni atoms, the use of Ir–Re alloy as a release agent coating for Ni–P plated moulds is expected to lead to a high degree of durability.
Design optimization of GaAs betavoltaic batteries
Authors: Chen Haiyanag , Jiang Lan , Chen Xuyuan
Published: May 2011

GaAs junctions are designed and fabricated for betavoltaic batteries. The design is optimized according to the characteristics of GaAs interface states and the diffusion length in the depletion region of GaAs carriers. Under an illumination of 10 mCi cm−2
63Ni, the open circuit voltage of the optimized batteries is about ∼0.3 V. It is found that the GaAs interface states induce depletion layers on P-type GaAs surfaces. The depletion layer along the P+PN+ junction edge isolates the perimeter surface from the bulk junction, which tends to significantly reduce the battery dark current and leads to a high open circuit voltage. The short circuit current density of the optimized junction is about 28 nA cm−2, which indicates a carrier diffusion length of less than 1 µm. The overall results show that multi-layer P+PN+ junctions are the preferred structures for GaAs betavoltaic battery design.
Radial liquid crystal alignment based on circular rubbing of a substrate coated with poly(N-vinyl carbazole) film
Authors: Chen Yuan-Di , Fuh Andy Ying-Guey , Liu Cheng-Kai , Cheng Ko-Ting
Published: May 2011

This paper presents a simple method to produce radial liquid crystal (LC) alignment layers using circular rubbing of poly(N-vinyl carbazole) (PVK) films. The produced layer can be used for fabricating axially symmetric homogeneous–radial, homeotropic–radial and radial–radial LC alignment devices by combining a rubbed PVK-coated substrate with another one with a desired LC alignment layer. The transmittance–voltage curves of the fabricated LC devices at various positions are measured to examine the uniformity of the alignment effect. Additionally, the PVK film does not absorb visible light, and can be operated at high temperatures.
Study of the optical response of Si-rich a-SiNx : H thin film near Si L2,3-edge using soft x-ray reflectivity
Authors: Singh Sarab Preet , Modi Mohammed H , Srivastava P
Published: May 2011

Angle-dependent soft x-ray reflectivity measurements in the photon energy range 82.67–248 eV near the Si L
2,3 absorption edge have been performed on Si-rich a-SiN
x
 : H (SRSN) thin film deposited by the Hg-sensitized photo-chemical vapour deposition technique. It is found that experimentally obtained δ (dispersion) values of the SRSN film lie in between that of pure silicon (Si) and silicon nitride (Si3N4). X-ray photoelectron spectroscopy measurements suggest that excess silicon is responsible for reducing optical constants values and hence by controlling the silicon amount one can tune the optical constants to desired values. We further compare the soft x-ray optical spectrum of the SRSN film with those of other silicon compounds such as silicon carbide (SiC) and silicon monoxide (SiO) near the Si L
2,3 edge region to shows its possibility as a prospective material for the next generation 13.5 nm (91.85 eV) node extreme ultraviolet (EUV) lithography technology.
A multiple network learning approach to capture system-wide condition-specific responses
Authors: Roy Sushmita , Werner-Washburne Margaret , Lane Terran
Published: May 2011

Motivation: Condition-specific networks capture system-wide behavior under varying conditions such as environmental stresses, cell types or tissues. These networks frequently comprise parts that are unique to each condition, and parts that are shared among related conditions. Existing approaches for learning condition-specific networks typically identify either only differences or only similarities across conditions. Most of these approaches first learn networks per condition independently, and then identify similarities and differences in a post-learning step. Such approaches do not exploit the shared information across conditions during network learning.

Results: We describe an approach for learning condition-specific networks that identifies the shared and unique subgraphs during network learning simultaneously, rather than as a post-processing step. Our approach learns networks across condition sets, shares data from different conditions and produces high-quality networks that capture biologically meaningful information. On simulated data, our approach outperformed an existing approach that learns networks independently for each condition, especially for small training datasets. On microarray data of hundreds of deletion mutants in two, yeast stationary-phase cell populations, the inferred network structure identified several common and population-specific effects of these deletion mutants and several high-confidence cases of double-deletion pairs, which can be experimentally tested. Our results are consistent with and extend the existing knowledge base of differentiated cell populations in yeast stationary phase.

Availability and Implementation: C++ code can be accessed from http://www.broadinstitute.org/~sroy/condspec/

Contact:  sroy@broadinstitute.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
The strength of chemical linkage as a criterion for pruning metabolic graphs
Authors: Zhou Wanding , Nakhleh Luay
Published: May 2011

Motivation: A metabolic graph represents the connectivity patterns of a metabolic system, and provides a powerful framework within which the organization of metabolic reactions can be analyzed and elucidated. A common practice is to prune (i.e. remove nodes and edges) the metabolic graph prior to any analysis in order to eliminate confounding signals from the representation. Currently, this pruning process is carried out in an ad hoc fashion, resulting in discrepancies and ambiguities across studies.

Results: We propose a biochemically informative criterion, the strength of chemical linkage (SCL), for a systematic pruning of metabolic graphs. By analyzing the metabolic graph of Escherichia coli, we show that thresholding SCL is powerful in selecting the conventional pathways' connectivity out of the raw network connectivity when the network is restricted to the reactions collected from these pathways. Further, we argue that the root of ambiguity in pruning metabolic graphs is in the continuity of the amount of chemical content that can be conserved in reaction transformation patterns. Finally, we demonstrate how biochemical pathways can be inferred efficiently if the search procedure is guided by SCL.

Contact:  wz4@rice.edu; nakhleh@rice.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Application of the Bayesian MMSE estimator for classification error to gene expression microarray data
Authors: Dalton Lori A. , Dougherty Edward R.
Published: May 2011

Motivation: With the development of high-throughput genomic and proteomic technologies, coupled with the inherent difficulties in obtaining large samples, biomedicine faces difficult small-sample classification issues, in particular, error estimation. Most popular error estimation methods are motivated by intuition rather than mathematical inference. A recently proposed error estimator based on Bayesian minimum mean square error estimation places error estimation in an optimal filtering framework. In this work, we examine the application of this error estimator to gene expression microarray data, including the suitability of the Gaussian model with normal–inverse-Wishart priors and how to find prior probabilities.

Results: We provide an implementation for non-linear classification, where closed form solutions are not available. We propose a methodology for calibrating normal-inverse-Wishart priors based on discarded microarray data and examine the performance on synthetic high-dimensional data and a real dataset from a breast cancer study. The calibrated Bayesian error estimator has superior root mean square performance, especially with moderate to high expected true errors and small feature sizes.

Availability: We have implemented in C code the Bayesian error estimator for Gaussian distributions and normal–inverse-Wishart priors for both linear classifiers, with exact closed-form representations, and arbitrary classifiers, where we use a Monte Carlo approximation. Our code for the Bayesian error estimator and a toolbox of related utilities are available at http://gsp.tamu.edu/Publications/supplementary/dalton11a. Several supporting simulations are also included.

Contact:  ldalton@tamu.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
TVNViewer: An interactive visualization tool for exploring networks that change over time or space
Authors: Curtis Ross E. , Yuen Amos , Song Le , Goyal Anuj , Xing Eric P.
Published: May 2011

Summary: The relationship between genes and proteins is a dynamic relationship that changes across time and differs in different cells. The study of these differences can reveal various insights into biological processes and disease progression, especially with the aid of proper tools for network visualization. Toward this purpose, we have developed TVNViewer, a novel visualization tool, which is specifically designed to aid in the exploration and analysis of dynamic networks.

Availability: TVNViewer is freely available with documentation and tutorials on the web at http://sailing.cs.cmu.edu/tvnviewer.

Contact:  epxing@cs.cmu.edu
Identification of prokaryotic small proteins using a comparative genomic approach
Authors: Samayoa Josue , Yildiz Fitnat H. , Karplus Kevin
Published: May 2011

Motivation: Accurate prediction of genes encoding small proteins (on the order of 50 amino acids or less) remains an elusive open problem in bioinformatics. Some of the best methods for gene prediction use either sequence composition analysis or sequence similarity to a known protein coding sequence. These methods often fail for small proteins, however, either due to a lack of experimentally verified small protein coding genes or due to the limited statistical significance of statistics on small sequences.

Our approach is based upon the hypothesis that true small proteins will be under selective pressure for encoding the particular amino acid sequence, for ease of translation by the ribosome and for structural stability. This stability can be achieved either independently or as part of a larger protein complex. Given this assumption, it follows that small proteins should display conserved local protein structure properties much like larger proteins. Our method incorporates neural-net predictions for three local structure alphabets within a comparative genomic approach using a genomic alignment of 22 closely related bacteria genomes to generate predictions for whether or not a given open reading frame (ORF) encodes for a small protein.

Results: We have applied this method to the complete genome for Escherichia coli strain K12 and looked at how well our method performed on a set of 60 experimentally verified small proteins from this organism. Out of a total of 11 407 possible ORFs, we found that 6 of the top 10 and 27 of the top 100 predictions belonged to the set of 60 experimentally verified small proteins. We found 35 of all the true small proteins within the top 200 predictions. We compared our method to Glimmer, using a default Glimmer protocol and a modified small ORF Glimmer protocol with a lower minimum size cutoff. The default Glimmer protocol identified 16 of the true small proteins (all in the top 200 predictions), but failed to predict on 34 due to size cutoffs. The small ORF Glimmer protocol made predictions for all the experimentally verified small proteins but only contained 9 of the 60 true small proteins within the top 200 predictions.

Contact:  jsamayoa@jhu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
MPEA—metabolite pathway enrichment analysis
Authors: Kankainen Matti , Gopalacharyulu Peddinti , Holm Liisa , Orešič Matej
Published: May 2011

Summary: We present metabolite pathway enrichment analysis (MPEA) for the visualization and biological interpretation of metabolite data at the system level. Our tool follows the concept of gene set enrichment analysis (GSEA) and tests whether metabolites involved in some predefined pathway occur towards the top (or bottom) of a ranked query compound list. In particular, MPEA is designed to handle many-to-many relationships that may occur between the query compounds and metabolite annotations. For a demonstration, we analysed metabolite profiles of 14 twin pairs with differing body weights. MPEA found significant pathways from data that had no significant individual query compounds, its results were congruent with those discovered from transcriptomics data and it detected more pathways than the competing metabolic pathway method did.

Availability: The web server and source code of MPEA are available at http://ekhidna.biocenter.helsinki.fi/poxo/mpea/.

Contact:  matti.kankainen@helsinki.fi

Supplementary information:  Supplementary data are available at Bioinformatics online.
A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes
Authors: Zhang Yong E. , Vibranovski Maria D. , Krinsky Benjamin H. , Long Manyuan
Published: May 2011

Motivation: Retrocopies are important genes in the genomes of almost all higher eukaryotes. However, the annotation of such genes is a non-trivial task. Intronless genes have often been considered to be retroposed copies of intron-containing paralogs. Such categorization relies on the implicit premise that alignable regions of the duplicates should be long enough to cover exon–exon junctions of the intron-containing genes, and thus intron loss events can be inferred. Here, we examined the alternative possibility that intronless genes could be generated by partial DNA-based duplication of intron-containing genes in the fruitfly genome.

Results: By building pairwise protein-, transcript- and genome-level DNA alignments between intronless genes and their corresponding intron-containing paralogs, we found that alignments do not cover exon–exon junctions in 40% of cases and thus no intron loss could be inferred. For these cases, the candidate parental proteins tend to be partially duplicated, and intergenic sequences or neighboring genes are included in the intronless paralog. Moreover, we observed that it is significantly less likely for these paralogs to show inter-chromosomal duplication and testis-dominant transcription, compared to the remaining 60% of cases with evidence of clear intron loss (retrogenes). These lines of analysis reveal that DNA-based duplication contributes significantly to the 40% of cases of single exon gene duplication. Finally, we performed an analogous survey in the human genome and the result is similar, wherein 34% of the cases do not cover exon–exon junctions. Thus, genome annotation for retrogene identification should discard candidates without clear evidence of intron loss.

Contact:  mlong@uchicago.edu; zhangy@uchicago.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.