bluuebunny/crossref_metadata_2025 huggingface dataset:
Origins of Disease Phobia
Authors: Bianchi G. N.
Published: January 2011

The literature on disease phobia is discussed and a controlled study of this variety of hypochondriasis is presented.

There were 30 disease phobic and 30 control subjects, in-patients of a general hospital psychiatric unit in Sydney. Controls were defined as lacking the symptoms ‘disease phobia’, ‘disease conviction’, ‘somatic preoccupation’ and ‘psychogenic pain’. Matching was one-for-one and concerned sex, age and occupational prestige.

In brief, the disease phobics were more anxious and self-pitying (current mental state). Before the illness they were more prone to inhibition of anger, bodily concern and low selfesteem (personality variables). As children they were more often weak, sickly and overprotected. Fifteen were youngest siblings versus only six of the controls. They gave a history of much family illness, substantiated by the findings of an excess of deaths among the mothers of disease phobics (life history characteristics). They reported an electrical current as a sensation at relatively low voltages and had low tolerance of pain (experimental measures).

A logical insight into the origins of disease phobia is provided by inter-relating the data from these four aspects of the investigations (Fig. 1). This matrix is interpreted in terms of the augmentation-reduction theory of Petrie.
Relationship between the Psychogalvanic Reflex and the Eysenck Personality Inventory N Score
Authors: Verghese Abraham
Published: January 2011

A psychogalvanic reflex (P.G.R.) study, conducted in the Department of Psychiatry, Christian Medical College, Vellore, India, is described. 20 subjects took part in this study They consisted of 10 members of the staff and 10 neurotic patients. All of them filled up the Eysenck Personality Inventory A form. A continuous P.G.R. tracing was recorded on a Grass 4-channel polygraph, before, during, and after a standard stress test (Progressive Matrices). A high N score differentiated the neurotic group from the normal group. P.G.R. changes did not differentiate the two groups. N score was significantly correlated to initial resistance change percentage (+0.568) and to initial log change conductance (−0.458). The implications of these findings are discussed.
Factor Structure and Norms for the Revised Behavior Problem Checklist in New Zealand Children
Authors: Aman Michael G. , Werry John S. , Fitzpatrick Joanne , Lowe Malcolm , Waters Jill
Published: January 2011

The Revised Behavior Problem Checklist (RBPC) is a recent expansion of the widely used Behavior Problem Checklist. This study attempted to replicate the factor structure of the RBPC, originally developed for U.S.A. children, and to establish norms for its use with New Zealand children. Two groups of children, aged five to 13 years, were rated on the scale by their parents. One was a clinic sample and comprised 266 patients attending two psychiatric clinics. The second was a random community sample of 267 children, from four census tracts in Auckland, selected to cover a range of socioeconomic strata representative of New Zealand. Factor analysis of the clinic data resulted in a factor structure similar to that found in American children. Only two of the six factors (Socialised Aggression and Psychotic Behaviour) differed to any degree. Using ratings from the community sample, norms were developed for screening and diagnostic purposes.
The Dexamethasone Suppression Test in the Puerperium
Authors: Greenwood Jim , Parker Gordon
Published: January 2011

A consecutive series of 45 women admitted to an obstetric unit were given the dexamethasone suppression test (DST) on days three to five post-partum, 82% being abnormal. The likelihood of an abnormal DST on one or both occasions increased linearly across the days of testing. Subjects completed the Beck self-report depression measure and the General Health Questionnaire at baseline and at six weeks. Baseline cortisol levels were not associated with baseline morbidity as assessed on the questionnaires and were not predictive of morbidity assessed at the six-week follow-up. It is concluded that the immediate post-partum period be included as a false-positive influence on the DST.
Differential Diagnosis and Treatment of Panic Disorder: A Medical Model Perspective
Authors: Vittone Bernard J. , Uhde Thomas W.
Published: January 2011

The authors present a review of existing literature along with new data regarding the phenomenology, differential diagnosis, course and treatment of panic disorder and agoraphobia. Panic attacks are viewed as central to the development of these disorders, and individual cognitive frameworks contribute to the manner in which a patient's symptoms evolve. An apparent though unclear relation to depressive states is described. Substance abuse may also be a consequence of recurrent panic attacks. A scheme towards differential diagnosis of panic disorder from other psychiatric and medical disorders is proposed. Personality characteristics of these patients vary considerably, but certain factors, such as dependency, are common. Family relations are often strained and assume importance in treatment. Data on the longitudinal course of illness is presented implying a relationship of panic disorder to both depression and stressful life events in many patients. Treatments that thus far seem most effective are pharmacological and behavioural approaches. Imipramine, MAO inhibitors, and alprazolam currently appear to be the most useful medications employed, although other agents may at times be useful alternatives. Dietary interventions, family therapy, and group and individual psychotherapy are also reviewed and discussed as adjunctive therapies in the treatment of panic disorder.
Treatment Outlines for the Management of Anxiety States
Authors: Andrews G.
Published: January 2011

The Quality Assurance Project is developing explicit and detailed treatment outlines for each of the major psychiatric disorders. Three sources of information are used: a meta-analysis of the treatment outcome literature, the opinions of a sample of practising psychiatrists, and the views of a panel of nominated experts. The recommendations for the treatment of anxiety states were as follows: Phenelzine and then the tricyclic antidepressants were the treatments of choice for panic disorder. Behaviour therapy—cognitive anxiety management, relaxation and hyperventilation control—being recommended as an essential adjunct to drug therapy. Relaxation and dynamic psychotherapy separately, or in combination, were the treatments of choice for generalised anxiety disorder with cognitive procedures being of value and benzodiazepines only being recommended for short-term use. In complicated cases of either panic disorder or generalised anxiety disorder a long-term supportive psychotherapeutic relationship was regarded as essential to ensure smooth progress in treatment. In adjustment disorder with anxious mood, procedures to permit adaptation to the stressor were recommended, while in post-traumatic stress disorder psychotherapeutic techniques to allow the trauma to be reexperienced and worked through were favoured.
Suicide in Association with Psychiatric Hospitalisation
Authors: Goldney Robert D. , Positano Sandro , Spence Neil D. , Rosenman Stephen J.
Published: January 2011

A review of 46 subjects who suicided after having contact with a psychiatric hospital is presented. There were 33 men and 11 women, both with a mean age of 37 years. In comparison with a control group, those who suicided had a greater number of hospital admissions, a greater length of hospitalisation, were more often unemployed, had a history of more previous suicide attempts, more often received the diagnosis of schizophrenia or manic depressive illness (depressed phase), were more often overtly depressed at their last contact, and were more often prescribed neuroleptic medications. Although these differences emerged, suicide is an infrequent event, and these factors lack specificity in prediction. The important association of psychiatric illness with subsequent suicide is noted.
A Case of Cerebral Systemic Lupus Erythematosus Treated with Methylprednisolone Pulse Therapy
Authors: Price John , Klestov Alex , Beacham Bronwen , Roberts Corinne
Published: January 2011

A case of cerebral systemic lupus erythematosus is presented. This was characterised by a combination of organic, persecutory and atypical hypomanic features. After a very stormy course on oral steroids, treatment with intravenous methylprednisolone pulse therapy was begun. Subsequently the patient experienced a prolonged remission. This outcome supports the value of such therapy in cerebral systemic lupus erythematosus.
Type a Coronary-Prone Behaviour Pattern and Pathological Narcissism
Authors: Condon John T.
Published: January 2011

Type A coronary-prone behaviour pattern exhibits many of the features of neurotic repetition compulsion. Thus, it is often maladaptive and tends to be compulsive, inflexible, irrational and ultimately non-satisfying. There is a notable similarity between the descriptions of Type A individuals in the behavioural literature and narcissistic individuals in the psychoanalytic literature. It is postulated that Type A individuals may have a deficient self-representation. This psychodynamic formulation of Type A as a variant of pathological narcissism has implications for assessment, prevention and management. In particular, it may help discriminate a sub-group of high achievers who are neurotically motivated and have abnormally high arousal. Only this sub-group may be at increased risk of coronary pathology.
Temperament and Psychiatric Disorder: The Genetic Contribution to Behaviour in Childhood
Authors: Graham Philip , Stevenson Jim
Published: January 2011

The studies stemming from the New York longitudinal study of temperament in childhood are summarised and conceptual difficulties and problems arising from them are described. An alternative model of temperament provided by Buss and Plomin is also considered. Finally, a new typology of temperament is proposed. It is based on the suggestion that ordinary, non-pathological behaviours, in extreme form, can be viewed as manifestations of emotional disorder, hyperactivity and antisocial disorder. Empirical evidence derived both from twin studies and from epidemiological investigations is put forward to support this view.
Did Schizophrenia Exist before the Eighteenth Century?
Authors: Ellard John
Published: January 2011

Madness has resisted a satisfactory categorisation for 2, 000 years or more. During the last century attempts to define and understand schizophrenia as an entity within that disorder have failed. This article explores some of the reasons why this may have happened, in particular considering whether the syndrome that we now call schizophrenia has changed in recent years and whether it existed at all four centuries ago. It is based on the author's experience and upon contemporary case histories.
Psychoanalysis Today
Authors: Smith Graeme C.
Published: January 2011

Psychoanalysis as a theory has permeated Western culture in a way that often no longer is conscious. Psychoanalysis as a practice has had a more visible and stormy progress. A similar fate has befallen behavioural, biological, cognitive and social psychology, and it is argued that the attractiveness of reductionism acts to prevent critical appraisal of psychoanalysis and of the other paradigms.
The International Classification of Impairments, Disabilities and Handicaps: Its Usefulness in Classifying and Understanding Biopsychosocial Phenomena
Authors: McFarlane Alexander C.
Published: January 2011

The International Classification of Impairments, Disabilities and Handicaps (ICIDH) was devetoped because of the growing awareness that ICD-9 failed to reflect many of the problems that people bring to health care systems. The ICIDH was designed to classify the consequences of disease such as the disruption of daily activity and the social disadvantage that accompany illness. However, since its introduction, the ICIDH has largely been ignored by psychiatry, despite its conceptual strength. In particular, it provides a framework for applying the biopsychosocial model and studying the phenomena of mental illness. The latter is an important issue because of clinical psychiatry's inherent weakness in distinguishing between symptoms of disease and the psychosociat consequences, a particular inadequacy of the DSM-III diagnostic criteria. The utility of the ICIDH is shown in the study of the phenomena of panic disorder and agoraphobia, where I conclude that agoraphobia should be classified as a disability/handicap and not a disorder.
Psychoanalysis and the Acquisition of Knowledge
Authors: Gold Stanley
Published: January 2011

From the myth of Prometheus to the trial of Galileo, history and literature are replete with examples of the clash between institutionally-bound power structures which exploit ignorance and ignore reality, and those that attempt to develop some movement towards scientific and personal truth. Within society as we know it, the genius or messiah figure and the establishment are bound together in an attempt to establish a relationship which can be of constructive relevance to both. The challenge of incorporating new and disruptive, though not necessarily disintegrative thought on the one hand, is contrasted with an uncompromising attack upon those who would lay claim to the previously exclusive rights of the established organisation and the power which accrued from them. Psychoanalysis today is joined in the battle with internal and external prohibitions against the acquisition of knowledge, which may in time point towards the truth of human personality, behaviour and existence.
The Brain and Higher Mental Function
Authors: Smith Graeme C.
Published: January 2011

Critical evaluation of biological theories of psychiatric disorder requires an understanding of current concepts of higher mental function and its related biology. Both the nature of the topic and the rapidity of advances in the field make it difficult to obtain an updated synthesis. Part I of this paper attempts to provide that by reviewing current concepts of the mind/body relationship, emotion, arousal, attention, consciousness and motivation. Part II considers those concepts in relation to recent work on the structure and function of the reticular, limbic and anterior cerebral systems. It is concluded that the model of the limbic system as subserving emotional life could now perhaps be set aside in favour of the model of a core set of chemically identified neurons in the reticular system being necessary but not sufficient to subserve higher mental function whilst also subserving other integrating functions for which no mental terminology is required. The problem of developing an eclectic theory of higher mental function that will embrace these concepts is discussed.
Attitudes of Psychiatric Patients and their Relatives to Involuntary Treatment
Authors: Adams Nicholas H.S. , Hafner R. Julian
Published: January 2011

In 1979 a Guardianship Board assumed responsibility in South Australia for the welfare of those mentally ill or handicapped people unable to look after their own health or safety, or to manage their own affairs. This study examines the attitudes to guardianship and involuntary treatment of 79 patients referred to the Board from a psychiatric hospital, all of whom were under guardianship at the time of the study. Forty-seven of their relatives took part in the project, which included measures of patients' psychiatric symptoms and relatives' punitiveness. Although almost 70% of patients objected to Guardianship in principle, they made more positive than negative statements about it. Nearly 60% rated involuntary treatment, including medication, as helpful. Patients reported a level of psychiatric symptoms less than half of that of a psychiatric outpatient sample. Relatives were strongly in favour of Guardianship, stating frequently that it allowed an improved relationship between themselves and the patient. Patients who believed that they were suffering from a mental illness were comparatively happy about being under Guardianship, and a belief that the patient was mentally ill was significantly associated with reduced ex-trapunitiveness in relatives.
Concordance with Recommendations in a Consultation-Liaison Psychiatry Service
Authors: Seward Louise N. , Smith Graeme C. , Stuart Geoffrey W.
Published: January 2011

We studied the concordance of physicians with the recommendations of psychiatric consultants in a sample of 270 consultations in a 400-bed general hospital. Of the patients about whom a consultation was sought, 37% had a past psychiatric history, and 67% were on psychotropic drugs. Twelve percent had Organic Mental Disorder, 35% Affective Disorder, and for 24% no DSM-Ill diagnosis could be made. The psychiatrist made psychotropic drug recommendations in 62%, and the physicians' concordance with this recommendation was 86%. The physician's discharge summary included a diagnosis which concorded with the psychiatrist's diagnosis in 53% of files. The psychiatrist recommended further investigations in only 5.2% of files.
The Fertility of HD-Affected Individuals in Tasmania
Authors: Pridmore Saxby A. , Adams Geoffrey C.
Published: January 2011

A study was conducted of the fertility (number of live births) of Huntington's disease (HD)-affected individuals compared to that of the general population using data from the 1986 Census of Population and Housing. HD-affected individuals were found to be at least as fertile as members of the general population. This finding supports earlier studies.
The National Mental Health Policy: Implications for Public Psychiatric Services in Australia
Authors: Whiteford Harvey , Macleod Bronwyn , Leitch Elizabeth
Published: January 2011

The Health Ministers of all Australian States, Territories and the Commonwealth endorsed National Mental Health Policy in April 1992 [1]. This Policy is intended to set clear direction for the future development of mental health services within Australia. The Policy recognises the high prevalence of mental health problems and mental disorders in the Australian community and the impact of these on consumers, carers, families and society as whole. It also clearly accepts the need to address the problems confronting the promotion of mental health and the provision of mental health services.
Genetic Linkage and Schizophrenia: Methods, Recent Findings and Future Directions
Authors: Mowry Bryan J. , Levinson Douglas F.
Published: January 2011

Family, twin and adoption studies have shown that familial clustering in schizophrenia is predominantly due to genetic factors. On the basis of segregation analyses of the illness distribution in relatives of patients, various models of the mode of transmission have been put forward but as yet there is no consensus. Linkage analysis based on molecular genetic techniques provides more direct approach to discovering precisely what is inherited (one gene, small number of genes or many genes?) that generates vulnerability to schizophrenia. To date there has been no sufficiently replicated finding of one or more linked genes and many methodological complexities remain. However, the rate of progress in addressing these issues gives hope that genetic linkage analysis of schizophrenia will provide some answers.
Interethnic Variations in the Presence of Schneiderian First Rank Symptoms
Authors: Coffey Guy J. , Mackinnon Andrew , Minas I. H.
Published: January 2011

Differences in the presence of Schneiderian First Rank Symptoms in first admission schizophrenic patients were examined in five subcultural groupings treated in the same facilities. Examination of the case notes of 212 patients revealed that first rank symptoms were most prevalent in the UK immigrant group and least frequently present in the Greek immigrant group. First rank symptoms were more prevalent in patients admitted recently, admitted voluntarily, and amongst those who had at least some command of English.
Association of Negative Symptoms with Tardive Dyskinesia in Schizophrenic Patients
Authors: Chiu Helen , Lau Joseph , Lam Linda , Shum Patrick
Published: January 2011

In recent years, great deal of interest has been focused on the association between negative symptoms of schizophrenia and tardive dyskinesia, but the literature is far from conclusive. Thirty-six schizophrenic patients with tardive dyskinesia and 76 without were surveyed using the Scale for Assessment of Negative Symptoms. On univariate analysis, the composite score and scores of certain subscales were associated with tardive dyskinesia, but this association was lost on multivariate analysis. After adjusting for confounding variables like age, education and antipsychotic dose, no association of negative symptoms and tardive dyskinesia was found.
Lithium-Associated Transient Thyrotoxicosis in 4 Chinese Women with Autoimmune Thyroiditis
Authors: Chow Chun-Chung , Lee Sing , Shek Chi-Chung , Wing Yun-Kwok , Ahuja Anil , Cockram Clive S.
Published: January 2011

Four Chinese female patients who suffered from manic-depressive disorder and underlying autoimmune thyroiditis developed transient episodes of thyrotoxicosis during maintenance lithium therapy. Endocrinologically speaking, three of them had “Hashitoxicosis”, while the other had silent lymphocytic thyroiditis. Albeit rare among Western patients, such lithium-associated thyroid dysfunctions appeared to be more likely to occur in Hong Kong Chinese. They seemed to involve multiple aetiological factors, such as autoimmune thyroid disease, the toxic and immunomodulatory roles of lithium and perhaps genetic and dietary factors. Because of their self-limiting nature, the importance of avoiding unnecessary and potentially deleterious antithyroid treatment is emphasised.
Lessons from a Mood Disorders Unit
Authors: Brodaty Henry , Harris Lynne , Wilhelm Kay , Hickie Ian , Boyce Philip , Mitchell Philip , Parker Gordon , Eyers Kerrie
Published: January 2011

Specialist treatment centres, such as the Mood Disorders Unit (MDU) at Prince Henry Hospital, Sydney, have developed in response to the high prevalence of mood disorders and their frequent persistence and treatment resistance. The MDU's assessment and treatment of patients from state-wide catchment area and its teaching and research effectiveness are reviewed. Of 479 patients assessed between 1985 and 1989, there were 304 with primary depressive disorders, of whom 154 were followed up by clinical assessment at 52 weeks and 231 by telephone interview at 3 1/2 years. At intake, 59% were tertiary referral patients and 88% were from outside the local area. Two-thirds were recovered 3 1/2 years later, despite the disorders having been generally severe and protracted. Treatment modality was associated primarily with diagnosis, but also with age and somewhat with the patient's personality and consultant psychiatrists' preferences. No consistent predictors of outcome were discerned. Specialist tertiary referral centres, such as the MDU, contribute significantly to treatment success, especially of difficult cases, and enrich teaching and research.
Helping Agency Contact for Emotional Problems in Childhood and Early Adolescence and the Risk of Later Disorder
Authors: Feehan Michael , McGee Rob , Stanton Warren R.
Published: January 2011

Despite waning enthusiasm for labelling theories in the development of psychopathology, it has been claimed that contact with professional agencies in childhood can be associated with increased levels of later problem behaviour. In this study, help-seeking by parents for children with behaviour problems was examined using birth cohort followed longitudinally to age 15 years. No evidence was found to support the hypothesis that agency contact increased the risk of later mental health disorder, either in childhood or adolescence. Rather, the results suggested that help-seeking was associated with reduction in both the risk of DSM-III disorder and problem behaviour scores, up to five years after agency contact.
Psychological Maladjustment among Homeless Adolescents
Authors: Schweitzer Robert D. , Hier Sally Jean
Published: January 2011

The prevalence of psychological maladjustment in homeless adolescents (n = 54) was compared to control group (n 58) in Brisbane, Australia using the Youth Self-Report Scale [1]. Overall, 74% of the homeless group and 22.4% of the control group scored within the clinical range on one or more of the clinical subscales. There was considerable diversity of symptomatology in the homeless group. Less than half of the homeless group were within the clinical range on both the delinquent subscale and the thought disorder subscale. Depressive, Aggressive and Somatic Complaints were also prevalent. The study challenges preconceived notions of simple relationship between adolescent homelessness and delinquency, and draws attention to the psychological needs of this group of adolescents.
Economic Impact of Outbreaks of Norovirus Infection in Hospitals
Authors: Lee Bruce Y. , McGlone Sarah M. , Bailey Rachel R. , Wettstein Zachary S. , Umscheid Craig A. , Muder Robert R.
Published: January 2011

Norovirus is highly infectious and can spread rapidly in healthcare settings, consuming resources and resulting in longer hospital stays. Although the economic impact of specific past outbreaks has been reported (eg, a 2007 outbreak of norovirus infection at Johns Hopkins Hospital cost an estimated $650,000), these costs may not be generalizable. We developed an economic computer simulation model to assist policy makers, hospital administrators, infection control professionals, and other healthcare workers in determining how much to invest in norovirus prevention and control interventions above and beyond existing infection control measures.
Survey of Patients' Knowledge and Opinions regarding the Use of Indwelling Urinary Catheters
Authors: Greer Steven F. , Sethi Ajay K. , Hecker Michelle T. , McKinney Brandy L. , Dumford Donald M. , Donskey Curtis J.
Published: January 2011

In a survey of patients with short-term indwelling urinary catheters, 47% were aware that catheters cause urinary tract infections, 89% believed that catheters were not overused, and 68% preferred catheter placement rather than use of a bedside commode, bedpan, or diaper. Patient education is needed regarding the risks of urinary catheters.
Infections in Children Receiving Extracorporeal Life Support
Authors: Tse-Chang Alena , Midodzi William , Joffe Ari R. , Robinson Joan L.
Published: January 2011

Objective.

To describe risk factors for and the outcome of infections in children receiving extracorporeal life support (ECLS) and to determine the need for removal of foreign bodies with bloodstream infections (BSIs) in children receiving ECLS.

Design.

Retrospective cohort study.

Setting.

Tertiary care children's hospital.

Patients.

Children receiving ECLS from May 1997 through May 2007.

Methods.

For patients with documented infections, medical records were examined for demographic, clinical, and laboratory details. Patients with and without documented infections were compared with regard to demographic characteristics and ECLS course.

Results.

One hundred seventeen patients underwent ECLS for a total of 878 days (median, 5.12 days). Thirty-five patients (29.9%) developed 55 infections, including 21 BSIs (38.2%), 20 urinary tract infections (36.4%), 6 ventilator-associated pneumonia episodes (10.9%), 2 viral infections (3.6%), and 6 miscellaneous infections (10.9%). The rates (in cases per 1,000 ECLS-days) were 23.9 for BSI, 22.8 for urinary tract infection, and 6.8 for ventilator-associated pneumonia. There were no significant differences in the demographic characteristics, indications for ECLS, or ECLS course between infected and uninfected patients, except for the median duration of ECLS (10.1 vs 3.8 days; P < .001). One death was attributed to infection. Resolution of BSI occurred without removal of foreign bodies in 18 (85.7%) of 21 children.

Conclusions.

Longer duration of ECLS was the only identified risk factor for infection. Mortality was not statistically significantly different between infected and uninfected patients. Most BSIs that occurred during ECLS cleared without removal of foreign bodies.
Tuberculosis among Families of Children with Suspected Tuberculosis and Employees at a Children's Hospital
Authors: Cruz Andrea T. , Medina Denise , Whaley Elaine M. , Ware Kathy M. , Koy Tjin H. , Starke Jeffrey R.
Published: January 2011

Children with tuberculosis are rarely contagious, but their caregivers may be. Only 7 (12%) of 59 children were potentially contagious, and 10 (17%) were accompanied by contagious adults. Screening caregivers was more cost-effective than performing employee contact investigations, with one-sixteenth the cost ($5,470 vs $88,323) and requiring screening of 35 times fewer persons.
Higher Cohen-Macaulay property of squarefree modules and simplicial posets
Authors: Yanagawa Kohji
Published: January 2011

Recently, G. Fløystad studied higher Cohen-Macaulay property of certain finite regular cell complexes. In this paper, we partially extend his results to squarefree modules, toric face rings, and simplicial posets. For example, we show that if (the corresponding cell complex of) a simplicial poset is

l
l

-Cohen-Macaulay, then its codimension one skeleton is

(
l
+
1
)

(l+1)

-Cohen-Macaulay.
BayesPeak—an R package for analysing ChIP-seq data
Authors: Cairns Jonathan , Spyrou Christiana , Stark Rory , Smith Mike L. , Lynch Andy G. , Tavaré Simon
Published: January 2011

Motivation: Identification of genomic regions of interest in ChIP-seq data, commonly referred to as peak-calling, aims to find the locations of transcription factor binding sites, modified histones or nucleosomes. The BayesPeak algorithm was developed to model the data structure using Bayesian statistical techniques and was shown to be a reliable method, but did not have a full-genome implementation.

Results: In this note we present BayesPeak, an R package for genome-wide peak-calling that provides a flexible implementation of the BayesPeak algorithm and is compatible with downstream BioConductor packages. The BayesPeak package introduces a new method for summarizing posterior probability output, along with methods for handling overfitting and support for parallel processing. We briefly compare the package with other common peak-callers.

Availability: Available as part of BioConductor version 2.6. URL: http://bioconductor.org/packages/release/bioc/html/BayesPeak.html

Contact:  jonathan.cairns@cancer.org.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automated bond order assignment as an optimization problem
Authors: Dehof Anna Katharina , Rurainski Alexander , Bui Quang Bao Anh , Böcker Sebastian , Lenhof Hans-Peter , Hildebrandt Andreas
Published: January 2011

Motivation: Numerous applications in Computational Biology process molecular structures and hence strongly rely not only on correct atomic coordinates but also on correct bond order information. For proteins and nucleic acids, bond orders can be easily deduced but this does not hold for other types of molecules like ligands. For ligands, bond order information is not always provided in molecular databases and thus a variety of approaches tackling this problem have been developed. In this work, we extend an ansatz proposed by Wang et al. that assigns connectivity-based penalty scores and tries to heuristically approximate its optimum. In this work, we present three efficient and exact solvers for the problem replacing the heuristic approximation scheme of the original approach: an A*, an ILP and an fixed-parameter approach (FPT) approach.

Results: We implemented and evaluated the original implementation, our A*, ILP and FPT formulation on the MMFF94 validation suite and the KEGG Drug database. We show the benefit of computing exact solutions of the penalty minimization problem and the additional gain when computing all optimal (or even suboptimal) solutions. We close with a detailed comparison of our methods.

Availability: The A* and ILP solution are integrated into the open-source C++ LGPL library BALL and the molecular visualization and modelling tool BALLView and can be downloaded from our homepage www.ball-project.org. The FPT implementation can be downloaded from http://bio.informatik.uni-jena.de/software/.

Contact:  anna.dehof@bioinf.uni-sb.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Facilitating a Small Group Teaching Session
Authors: Knox Richard
Published: January 2011

The small group is one of the more common settings in which you may find yourself teaching. It can take many forms from the breakout group on a vocational training scheme day, to an undergraduate ethics discussion, or a newly diagnosed patient information event. The skill of facilitation has many transferable attributes, including those associated with chairing a meeting. A greater understanding of the role of the facilitator can also help you get the most out of education events that you attend as a user. This article aims to equip you with seven carefully considered tools to enhance your facilitation skills and also discusses ways in which you can actually demonstrate those abilities.
Non-Cystic Fibrosis Bronchiectasis
Authors: Mydin Helmy Haja , De Soyza Anthony
Published: January 2011

Bronchiectasis is a term that encompasses the clinical manifestation and pathological findings of patients with chronic bronchial inflammation leading to permanent bronchial architectural distortion. This structural change is the underlying cause for recurrent lower respiratory tract infections (LRTIs) and the condition's characteristic symptoms. The aim of this article is to provide a concise overview of non-cystic fibrosis bronchiectasis (henceforth termed ‘bronchiectasis’ for the purpose of this article) based on the recently published British Thoracic Society (BTS) guidelines and the role of primary care in its management.
Isoflurane Activates Intestinal Sphingosine Kinase to Protect against Renal Ischemia–Reperfusion-induced Liver and Intestine Injury
Authors: Kim Minjae , Park Sang Won , Kim Mihwa , D'Agati Vivette D. , Lee H. Thomas
Published: January 2011

Background

Renal ischemia-reperfusion injury (IRI) is a major cause of acute kidney injury and often leads to multiorgan dysfunction and systemic inflammation. Volatile anesthetics have potent antiinflammatory effects. We aimed to determine whether the representative volatile anesthetic isoflurane protects against acute kidney injury-induced liver and intestinal injury and to determine the mechanisms involved in this protection.

Methods

Mice were anesthetized with pentobarbital and subjected to 30 min of left renal ischemia after right nephrectomy, followed by exposure to 4 h of equianesthetic doses of pentobarbital or isoflurane. Five hours after renal IRI, plasma creatinine and alanine aminotransferase concentrations were measured. Liver and intestine tissues were analyzed for proinflammatory messenger RNA (mRNA) concentrations, histologic features, sphingosine kinase-1 (SK1) immunoblotting, SK1 activity, and sphingosine-1-phosphate concentrations.

Results

Renal IRI with pentobarbital led to severe renal, hepatic, and intestinal injury with focused periportal hepatocyte vacuolization; small-intestinal apoptosis; and proinflammatory mRNA up-regulation. Isoflurane protected against renal IRI and reduced hepatic and intestinal injury via induction of small-intestinal crypt SK1 mRNA, protein and enzyme activity, and increased sphingosine-1-phosphate. We confirmed the importance of SK1 because mice treated with a selective SK inhibitor or mice deficient in the SK1 enzyme were not protected against hepatic and intestinal dysfunction with isoflurane.

Conclusions

Isoflurane protects against multiorgan injury after renal IRI via induction of the SK1/sphingosine-1-phosphate pathway. Our findings may help to unravel the cellular signaling pathways of volatile anesthetic-mediated hepatic and intestinal protection and may lead to new therapeutic applications of volatile anesthetics during the perioperative period.
Nanometric depth resolution from multi-focal images in microscopy
Authors: Dalgarno Heather I. C. , Dalgarno Paul A. , Dada Adetunmise C. , Towers Catherine E. , Gibson Gavin J. , Parton Richard M. , Davis Ilan , Warburton Richard J. , Greenaway Alan H.
Published: January 2011

We describe a method for tracking the position of small features in three dimensions from images recorded on a standard microscope with an inexpensive attachment between the microscope and the camera. The depth-measurement accuracy of this method is tested experimentally on a wide-field, inverted microscope and is shown to give approximately 8 nm depth resolution, over a specimen depth of approximately 6 µm, when using a 12-bit charge-coupled device (CCD) camera and very bright but unresolved particles. To assess low-flux limitations a theoretical model is used to derive an analytical expression for the minimum variance bound. The approximations used in the analytical treatment are tested using numerical simulations. It is concluded that approximately 14 nm depth resolution is achievable with flux levels available when tracking fluorescent sources in three dimensions in live-cell biology and that the method is suitable for three-dimensional photo-activated localization microscopy resolution. Sub-nanometre resolution could be achieved with photon-counting techniques at high flux levels.
Modelling the initial phase of an epidemic using incidence and infection network data: 2009 H1N1 pandemic in Israel as a case study
Authors: Katriel G. , Yaari R. , Huppert A. , Roll U. , Stone L.
Published: January 2011

This paper presents new computational and modelling tools for studying the dynamics of an epidemic in its initial stages that use both available incidence time series and data describing the population's infection network structure. The work is motivated by data collected at the beginning of the H1N1 pandemic outbreak in Israel in the summer of 2009. We formulated a new discrete-time stochastic epidemic SIR (susceptible-infected-recovered) model that explicitly takes into account the disease's specific generation-time distribution and the intrinsic demographic stochasticity inherent to the infection process. Moreover, in contrast with many other modelling approaches, the model allows direct analytical derivation of estimates for the effective reproductive number (Re) and of their credible intervals, by maximum likelihood and Bayesian methods. The basic model can be extended to include age–class structure, and a maximum likelihood methodology allows us to estimate the model's next-generation matrix by combining two types of data: (i) the incidence series of each age group, and (ii) infection network data that provide partial information of ‘who-infected-who’. Unlike other approaches for estimating the next-generation matrix, the method developed here does not require makinga prioriassumptions about the structure of the next-generation matrix. We show, using a simulation study, that even a relatively small amount of information about the infection network greatly improves the accuracy of estimation of the next-generation matrix. The method is applied in practice to estimate the next-generation matrix from the Israeli H1N1 pandemic data. The tools developed here should be of practical importance for future investigations of epidemics during their initial stages. However, they require the availability of data which represent a random sample of the real epidemic process. We discuss the conditions under which reporting rates may or may not influence our estimated quantities and the effects of bias.
Optimality of the Münch mechanism for translocation of sugars in plants
Authors: Jensen K. H. , Lee J. , Bohr T. , Bruus H. , Holbrook N. M. , Zwieniecki M. A.
Published: January 2011

Plants require effective vascular systems for the transport of water and dissolved molecules between distal regions. Their survival depends on the ability to transport sugars from the leaves where they are produced to sites of active growth; a flow driven, according to the Münch hypothesis, by osmotic gradients generated by differences in sugar concentration. The length scales over which sugars are produced (
L
leaf
) and over which they are transported (
L
stem
), as well as the radius
r
of the cylindrical phloem cells through which the transport takes place, vary among species over several orders of magnitude; a major unsettled question is whether the Münch transport mechanism is effective over this wide range of sizes. Optimization of translocation speed predicts a scaling relation between radius
r
and the characteristic lengths as
r
∼ (
L
leaf
L
stem
)
1/3
. Direct measurements using novel
in vivo
techniques and biomimicking microfluidic devices support this scaling relation and provide the first quantitative support for a unified mechanism of sugar translocation in plants spanning several orders of magnitude in size. The existence of a general scaling law for phloem dimensions provides a new framework for investigating the physical principles governing the morphological diversity of plants.
Collagen gel three-dimensional matrices combined with adhesive proteins stimulate neuronal differentiation of mesenchymal stem cells
Authors: Lee Jae Ho , Yu Hye-Sun , Lee Gil-Su , Ji Aeri , Hyun Jung Keun , Kim Hae-Won
Published: January 2011

Three-dimensional gel matrices provide specialized microenvironments that mimic native tissues and enable stem cells to grow and differentiate into specific cell types. Here, we show that collagen three-dimensional gel matrices prepared in combination with adhesive proteins, such as fibronectin (FN) and laminin (LN), provide significant cues to the differentiation into neuronal lineage of mesenchymal stem cells (MSCs) derived from rat bone marrow. When cultured within either a three-dimensional collagen gel alone or one containing either FN or LN, and free of nerve growth factor (NGF), the MSCs showed the development of numerous neurite outgrowths. These were, however, not readily observed in two-dimensional culture without the use of NGF. Immunofluorescence staining, western blot and fluorescence-activated cell sorting analyses demonstrated that a large population of cells was positive for NeuN and glial fibrillary acidic protein, which are specific to neuronal cells, when cultured in the three-dimensional collagen gel. The dependence of the neuronal differentiation of MSCs on the adhesive proteins containing three-dimensional gel matrices is considered to be closely related to focal adhesion kinase (FAK) activation through integrin receptor binding, as revealed by an experiment showing no neuronal outgrowth in the FAK-knockdown cells and stimulation of integrin β1 gene. The results provided herein suggest the potential role of three-dimensional collagen-based gel matrices combined with adhesive proteins in the neuronal differentiation of MSCs, even without the use of chemical differentiation factors. Furthermore, these findings suggest that three-dimensional gel matrices might be useful as nerve-regenerative scaffolds.
Slowing the evolution of insecticide resistance in mosquitoes: a mathematical model
Authors: Gourley Stephen A. , Liu Rongsong , Wu Jianhong
Published: January 2011

A big problem in malaria control is the rapidity with which mosquitoes can develop resistance to insecticides. The possibility of creating evolution-proof insecticides is therefore of considerable interest. Biologists have suggested that effective malaria control, with only weak selection for insecticide resistance, could be achieved if insecticides target only old mosquitoes that have already laid most of their eggs. The strategy aims to exploit the fact that most malarial mosquitoes do not live long enough to transmit the disease. We derive, analyse and compare two mathematical models, one for an insecticide that kills on exposure, and the other for an insecticide that targets only older mosquitoes. Both models predict that insecticide-resistant mosquitoes will become dominant over time but, very importantly, this occurs on a very much slower time scale when the insecticide only affects older mosquitoes. We present analytical results on linear and global stability of the non-trivial equilibrium in which only the resistant mosquito strain is present, together with a theorem comparing the rates of convergence for the two models. Numerical simulations show that the effect of targeting only old mosquitoes on the evolution of resistance is dramatic.
Scale-invariant filtering design and analysis for edge detection
Authors: Mahmoodi Sasan
Published: January 2011

Existing edge detection filters work well on straight edges but make significant errors near sharp corners by producing rounded corners. This is due to the fact that the edge maps produced by these filters are scale variant. We enhance Canny’s optimality criteria to incorporate detection performance near corners as an explicit design objective. The resulting optimal filter, termed ‘Bessel integral filter’, can be derived analytically and exhibits superior performance over recent alternatives, both in terms of numerical accuracy and experimental fidelity. A noise-free localization index is also derived here to account for the detection accuracy of discontinuities forming sharp corners in the absence of noise. We prove here that edges detected by the filters that are not optimal with respect to this noise-free localization index are scale variant. However, the Bessel integral filter proposed here is optimal with respect to the noise-free localization index and therefore it is a scale-invariant filter.
The ‘non-Kerrness’ of domains of outer communication of black holes and exteriors of stars
Authors: Bäckdahl Thomas , Valiente Kroon Juan A.
Published: January 2011

In this paper, we construct a geometric invariant for initial datasets for the vacuum Einstein field equations

, such that

is a three-dimensional manifold with an asymptotically Euclidean end and an inner boundary

with the topology of the 2-sphere. The hypersurface

can be thought of being in the domain of outer communication of a black hole or in the exterior of a star. The geometric invariant vanishes if and only if

is an initial dataset for the Kerr spacetime. The construction makes use of the notion of Killing spinors and of an expression for a
Killing spinor candidate
, which can be constructed out of concomitants of the Weyl tensor.
Genetic differentiation and the evolution of cooperation in chimpanzees and humans
Authors: Langergraber Kevin , Schubert Grit , Rowney Carolyn , Wrangham Richard , Zommers Zinta , Vigilant Linda
Published: January 2011

It has been proposed that human cooperation is unique among animals for its scale and complexity, its altruistic nature and its occurrence among large groups of individuals that are not closely related or are even strangers. One potential solution to this puzzle is that the unique aspects of human cooperation evolved as a result of high levels of lethal competition (i.e. warfare) between genetically differentiated groups. Although between-group migration would seem to make this scenario unlikely, the plausibility of the between-group competition model has recently been supported by analyses using estimates of genetic differentiation derived from contemporary human groups hypothesized to be representative of those that existed during the time period when human cooperation evolved. Here, we examine levels of between-group genetic differentiation in a large sample of contemporary human groups selected to overcome some of the problems with earlier estimates, and compare them with those of chimpanzees. We find that our estimates of between-group genetic differentiation in contemporary humans are lower than those used in previous tests, and not higher than those of chimpanzees. Because levels of between-group competition in contemporary humans and chimpanzees are also similar, these findings suggest that the identification of other factors that differ between chimpanzees and humans may be needed to provide a compelling explanation of why humans, but not chimpanzees, display the unique features of human cooperation.