bluuebunny/crossref_metadata_2025 huggingface dataset:
Living in a self‐organized house in the early psychosis treatment
Authors: Orsucci F. , Camillacci A. M. , Pasqualini R. , Verucci M.
Published: October 2010

The self‐organized house (SOH) is a resident structure with light outpatient assistance. We have had a long time experience of these structures in the rehabilitation treatment of chronic psychotics. Our more recent experience is to use these kind of structure for the early treatment, in the subacute phases. The patient is treated for several years, separated and protected from his family. Family therapy is started later. The flexibility of protection, therapies, and social committments allow a different perspective in the treatment of early psychosis. Several single cases, and study on a small sample group are presented.
The therapeutic alliance in early psychosis
Authors: Bentall R. , Tarrier N. , Lewis S. , Haddock G. , Kinderman P. , Kingdon D. ,   the SoCRATES team
Published: October 2010

Research with nonpsychotic patients has indicated that the therapeutic alliance makes an important contribution to outcome of psychological treatments. Although recent years have seen a resurgence of enthusiasm for psychotherapeutic interventions for psychotic patients, particularly following the publication of large‐scale RCTs of cognitive‐behaviour therapy (CBT) for schizophrenia patients, there have been few attempts to assess the contribution that the patient–therapist relationship makes to these interventions, which have been usually described in terms of particular techniques. However, in a study of psychodynamic therapy for chronic schizophrenia patients, Frank and Gunderson (1990) reported that patients were slow to form an adequate alliance, although the quality of the alliance was a predictor of long‐term outcome.

In this paper, we will review evidence from previous studies, and present data on the therapeutic alliance and other process variables taken during a large randomized controlled trial of CBT for first and second episode schizophrenia patients (the SoCRATES study). A total of 315 patients entered the study, and were randomized to treatment as usual, supportive counselling or CBT, with a 5‐week therapy envelope commencing within 2 weeks of admission to hospital. Baseline and follow‐up assessments were conducted by psychiatrists blind to group assignment, and 75% of the patients were retained in the study at 18 month follow‐up. We have reported the main outcome data elsewhere; statistically significant but modest benefits were found for both CBT and counselling. Therapeutic alliance measures were completed by both patients and therapists in thetwo psychological treatment groups at the third and 10th session. All measures had acceptable reliability but therapist assessments of the alliance correlated poorly with patients' perceptions. Both patient and therapist alliance ratings at session 3 predicted duration of treatment. Duration of treatment, in turn, predicted therapy response. The findings indicate the importance of investigating process variables as mediators of response to treatments for early psychosis.
Assessing prolonged recovery in first‐episode psychosis
Authors: Wong L. , Edwards J. , Harris M. , Harrigan S. , Elkins K.
Published: October 2010

The Early Psychosis Prevention and Intervention Centre (EPPIC) is a comprehensive, specialized treatment service for individuals residing in the western metropolitan region of Melbourne who are experiencing their first psychotic episode. A subprogramme of EPPIC, the Treatment Resistance Early Assessment Team (TREAT), has been developing a framework for the management of individuals experiencing ‘prolonged recovery’ in early psychosis. TREAT is a consultation team that provides technical assistance to clinicians within EPPIC, comprising senior clinicians with expertise in the biopsychosocial treatment of early psychosis and persisting positive and negative symptoms. A system has recently been set up within the TREAT framework to routinely assess clinical and functional outcomes of these clients using standardized instruments. Case managers are trained to conduct assessments at multiple timepoints over the duration of their clients' treatment at EPPIC. A summary will be presented on the current sample (n=15) and examples of clinician and client feedback reports will be illustrated. Discussion is also provided on the development of training, procedures and materials to enhance integration of clinician and client outcome measures into routine clinical practice.
Experience of caregiving amongst caregivers of first psychotic patients: a preliminary study
Authors: Chan R. , Lau D. , Lo M. , Hung S. F. , Chen E.
Published: October 2010

This study aimed to investigate the dimensions of the Chinese version of the Experience of Caregiving Inventory (ECI) in caregivers of people with early onset psychosis. The ECI was administered to 105 primary caregivers of people with early onset psychosis. A preliminary analysis of the responses was carried out using a principal components analysis (PCA) to identify the major dimensions. A total of 19 factors with eigenvalues greater than 1 was identified, and accounted for 73.12% of the total variance. Then, PCAs were run for a 6‐, 8‐, and 10‐factor solutions with the criteria of items loading 0.5 or higher on only one factor and separated by at least 0.1 from its loading on any other. Many distinct dimensions emerged, the best coverage requiring a 8‐factor solution (42 items accounting for 41.9% of the total variance). These factors were emotional disturbance and negativism, positive personal experiences, dependency, loss, stigma, problems with services, good aspects of relationship, and need to back up. The preliminary findings suggest a shorter version of the ECI may best fit for the Hong Kong Chinese context.
Promoting education, advocacy and support: the Canadian experience
Authors: Lines E.
Published: October 2010

For the past 3 years, the Canadian Mental Health Association (CMHA), a national voluntary organization, has coordinated an early psychosis intervention project intended to raise awareness, enhance family coping skills and promote the availability of and access to appropriate early psychosis services across Canada. Funded by Health Canada, this project has achieved breadth and depth of impact through Canada‐wide networking and dissemination of resource materials coupled with targeted local‐level activities at three CMHA sites. With a strong orientation toward increasing community capacity to understand, identify and respond to first episode psychosis, project activities have included: creating and broadly distributing print materials in English and French (hard copy and web) conducting educational workshops with community members and gatekeepers identifying advocacy opportunities and pursuing advocacy initiatives regarding policy and practice and supporting the development of first episode family networks across Canada and with them, creating and disseminating innovative family support resource materials. This poster session will present the process, products and outcomes of the project which can serve as a valuable model of a national level initiative and its evolution.
Reactance and treatment compliance in schizophrenia
Authors: Sellwood W. , Tarrier N.
Published: October 2010

A variety of factors are related to noncompliance in schizophrenia. However, little attention has been paid to what causes noncompliance. Reactance may be important. However, the direction of the observed relationship between reactance, freedom of choice and taking medication has not been confirmed. 95 college students were asked to read a story about an individual suffering from their first episode. There were two possible endings, one in which treatment was presented with little freedom of choice and one in which there was a high degree of freedom of choice. Participants also completed measures of their reactance and a rating of their likelihood of taking medication if they had experienced the circumstances described in the story. Reactance prone participants rated themselves as being less likely to take medication if their freedom of choice was restricted. Restriction of freedom of choice for nonreactance prone participants had no effect on their compliance ratings. Thus restricting patients' freedom of choice, early in their illnesses, may cause them to be noncompliant if they are prone to reactance. The relevance of these findings to clinical situations is discussed together with the limitations of the study.
Diagnoses at the first psychotic episode and cognitive functioning
Authors: Addington J. , Addington D.
Published: October 2010

Objectives  To determine the relationship between diagnosis and cognitive functioning in a first‐episode sample.

Methods  175 subjects were diagnosed (SCID) on admission to a comprehensive treatment programme for early psychosis and 1 year later. Symptoms (PANSS), social functioning and cognitive functioning (using a comprehensive cognitive battery) were assessed initially and at 1 year. Subjects were divided into three groups: (1) Stable diagnosis of schizophrenia over 1 year (n=84). (2) Initial diagnosis of schizophreniform, brief psychotic disorder, substance induced psychosis or psychosis NOS but who met criteria for schizophrenia at 1 year (n=49) and (3) Stable diagnosis over 1 year of schizophreniform, brief psychotic disorder, substance induced psychosis or psychosis NOS (n=44).

Results  There were significant differences amongst the three groups at both assessment periods in positive and negative symptoms and social functioning. There were no differences amongst the groups in cognitive functioning.

Conclusions  Individuals with psychotic disorders who do not go on to develop schizophrenia do not differ significantly in neurocognition from those who do develop schizophrenia, although they may have advantages in other areas.
Changes in appearance and psychosis
Authors: Campo J. M. L. G. Á. , Nijman H. , Merckelbach H. L. G. J. , Frederikx M.
Published: October 2010

Anecdotal reports suggest that drastic changes in physical appearance may signal decompensation in schizophrenic patients. The current study sought to explore the association between changes in appearance and psychotic vulnerability in a systematic fashion. 171 undergraduates completed the Physical Appearance Scale (PAS) that assesses frequency and nature ofchanges in outlooks, along with a Schizotypy Scale (STA), the Maudsley Obsessive Compulsive Inventory (MOCI), the Fear Questionnaire (FQ), and the Beck Depression Inventory (BDI). A modest but significant correlation was found between Physical Appearance Scale scores and STA‐scores. For the other symptom measures (i.e. MOCI, FQ and BDI), no association with changes in physical appearance emerged. The findings suggest that drastic changes of the physical are specifically linked to schizotypal dispositions and may point to a underlying vulnerability for developing schizophrenia. The clinical implications of the connection between marked changes in outlooks and psychosis are addressed.
Gender identity disorders as a secondary symptom of psychosis
Authors: Campo J. M. L. G. Á , Nijman H. , Evers C. , Merckelbach H. L. G. J. , Decker I.
Published: October 2010

In The Netherlands it has recently become possible for transsexual patients to receive hormonal treatment from the onset of puberty to prevent pubertal development. From 16 years of age onwards, gender adjustment can be initiated by administration of hormones of the opposite sex. Surgical treatment can be offered once the patient reaches 18 years of age. Although such treatment will only be initiated with reticence and after a long phase of intense diagnostic screening, the question arises whether a clear differentiation can be made between pure gender identity disorders and secondary transsexual feelings that are part of an ongoing psychopathological development, such as schizophrenia. The potential diagnostic confusion is illustrated by a case history of a male schizophrenic patient. This patient had been treated hormonally for transsexualism for years before acute psychotic decompensation occurred. Neuroleptic treatment of the psychosis rapidly reduced the psych‐otic symptoms. In retrospect, the patient regards his transsexual period as a ‘mistake’. Delusions about one's physical appearance and the urge to drastically change the way one looks appear to be relatively common in patients suffering from schizophrenia.
Schizophrenia and drastic changes in hairstyle
Authors: Campo J. M. L. G. Á. , Merckelbach H. L. G. J.
Published: October 2010

The current study evaluated whether drastic changes in hairstyle are associated with a diagnosis of schizophrenia. In a sample of 286 hospitalized psychiatric patients, it was found that manipulation of hairstyle is more frequently seen in schizophrenic or schizophreni‐form patients than in other diagnostic subgroups. Furthermore, the data suggest that there is a specific connection between schizophrenia of the disorganized type and drastic changes in hairstyle. The role of these changes in the phenomenology of schizophrenia is discussed.
WSFEPP: neuropsychological function and diagnosis in early psychosis
Authors: Fitzgerald D. , Lucas S. , Redoblado M. A. , Brennan J. , Anderson J. , Sanbrook M. , Taylor A. , Harris A.
Published: October 2010

Objective  This study aimed to examine whether neuropsychological profiles of young first‐episode psychosis (FEP) patients varied according to diagnosis.

Method  A sample of 94 FEP patients aged 13–25 were recruited as part of The Western Sydney First Episode Psychosis Project. Subjects completed a comprehensive battery of tests, grouped into 10 cognitive domains. Differences in cognitive profiles were examined in three diagnostic groups (schizophrenia, mood disorders, mixed psychosis) and compared to healthy controls. Correlations between neuropsychological deficits and clinical characteristics were explored.

Results  Patterns of deficit were similar across diagnostic categories, but areas of selective deficit differentiated psychotic mood disorders from schizophrenia and other psychosis. Results indicated greater deficits in verbal learning and memory for schizophrenia than psychotic mood disorders. The Mood disorders group demonstrated selective deficits only on speeded processing tasks. Negative symptoms were associated with poorer neuropsychological functioning.

Conclusions  Results confirm that significant cognitive deficits are evident in early psychosis and are present regardless of traditional diagnostic categorizations. However, results indicate that schizophrenia and mood disorders can be distinguished on the basis of areas of selective deficit.
Neuropsychological functioning and diagnosis in early psychosis
Authors: Fitzgerald D. , Lucas S. , Redoblado M. A. , Brennan J. , Anderson J. , Sanbrook M. , Taylor A. , Harris A.
Published: October 2010

Objective  This study aimed to examine whether neuropsychological profiles of young first‐episode psychosis (FEP) patients varied according to diagnosis.

Methods  A sample of 94 FEP patients aged 13–25 were recruited as part of The Western Sydney First Episode Psychosis Project. Subjects completed a comprehensive battery of tests, grouped into 10 cognitive domains. Differences in cognitive profiles were examined in three diagnostic groups (schizophrenia, mood disorders, mixed psychosis) and compared to healthy controls. Correlations between neuropsychological deficits and clinical characteristics were explored.

Results  Patterns of deficit were similar across diagnostic categories, but areas of selective deficit differentiated psychotic mood disorders from schizophrenia and other psychosis. Results indicated greater deficits in verbal learning and memory for schizophrenia than psychotic mood disorders. The Mood disorders group demonstrated selective deficits only on speeded processing tasks. Negative symptoms were associated with poorer neuropsychological functioning.

Conclusions  Results confirm that significant cognitive deficits are evident in early psychosis and are present regardless of traditional diagnostic categorizations. However, results indicate that schizophrenia and mood disorders can be distinguished on the basis of areas of selective deficit.
Duration of untreated psychosis: impact on 2‐year outcome
Authors: Addington J. , Van Mastrigt S. , Addington D.
Published: October 2010

Evidence demonstrating the predictive value of a long duration of untreated psychosis (DUP) remains equivocal. We assessed the impact of DUP on outcome over a 2‐year period in 203 first episode patients in an early psychosis programme. Symptoms (PANSS) were assessed every 3 months and functional outcome (QOL), neurocognitive functioning and relapse rates were assessed annually. Median DUP was 26 weeks, mean DUP was 80 weeks, mean log10 DUP was 23 weeks. Long DUP was significantly associated with positive symptoms (P < 0.001), and quality of life (P < 0.01) in the first year. Since there are no strong a priori grounds for a ‘cutoff’ level for long DUP, we compared those who were in remission (i.e. no positive symptom score greater than 3 on the PANSS) with those who had failed to achieve remission by 6 months. Results were that those who had failed to achieve remission of positive symptoms after 6 months of a comprehensive treatment approach had a significantly longer DUP (P < 0.001). Thus, in this sample of first episode subjects receiving optimal treatment DUP was associated with a poorer recovery.
Thought disorder prior to schizophrenia‐related vs. affective psychosis
Authors: Ott S. L. , Erlenmeyer‐Kimling L. , Roberts S.
Published: October 2010

Data from the New York High‐Risk Project were used to study prodromal symptoms in subjects age 9, years before some of them developed psychotic disorders. We rated thought disorder from videotaped interviews (total n=123). Previous analyses showed elevated scores in subjects with adulthood schizophrenia‐related psychosis (n=9), a group including individuals with schizophrenia (Sz, n=4) and schizoaffective disorder, mainly Sz (SAS, n=5). However, high scores were observed primarily in subjects with SAS.

To examine whether there is an association of thought disorder with psychosis in combination with affective disturbance, we examined means of three patients with adulthood affective psychosis (AffP), and found that none exhibited thought disorder in childhood. Thus, thought disorder was not present in subjects with AffP, moderately so in those with Sz, and high in those with SAS. An interpretation of these results seems, considering the sample sizes, speculative, in spite of statistical significance.

We were able to expand the sample to total n=255, with adulthood SRP n=14, and AffP n=9. We will present these analyses and further discuss thought disorder prior to affective and schizophrenia‐related psychosis.
Catatonic stupor induced by neuroleptic in adolescent
Authors: Askenazy F. , Lestideau K. , Myquel M. , Darcourt G. , Lecrubier Y.
Published: October 2010

We present a case report of neuroleptic malignant syndrome with catatonic state (CS) and without pyrexia in a 15‐year‐old‐girl. The onset was acute without previous history of psychotic symptoms. The neuroleptic malignant syndrome occurred after monotherapy with Loxapine (150 mg/day) during 15 days, followed by haloperidol (22.5 mg/day). After an improvement of hallucinatory symptoms, she presents a CS 24 days after a first dose of haloperidol. We describe the case history, and the management of this rare syndrome associated with a high mortality rate. Treatment was medical (parental nutrition hydratation) with intravenous clonazepram.

Organic (EEG and MRI abnormalities) and psychiatric symptoms largely overlapped from the onset of CS. Clinical state was characterized by prominent auditory hallucinations and visions. Family history was remarkable for alcoholism, violence, sexual trauma and neurological pathology. Clinical interview released the presence of auditory hallucinations in some young relatives.

This case report revealed by: (1) interactions between organic and psychiatric syndrome in catatonia, (2) the possible prodomal function of auditory hallucination in child, (3) the necessity of focusing on relatives in schizophrenia.
DUP in first‐episode schizophrenia and its early prognosis in Japan
Authors: Yamazawa R. , Mizuno M. , Nemoto T. , Watanabe K. , Yamashita C. , Oda K. , Chino B. , Kashima H.
Published: October 2010

DUP of first‐episode schizophrenia patients has recently been drawing a lot of attention, but there is no investigation in relation to early prognosis in Japan. The duration of first admission and neuroleptic dosage in 1 year after prescribing first neuroleptics have been studied.

Subjects and method  83 consecutive patients of neuroleptic naïve first‐episode schizophrenia from two hospitals were investigated on its mean DUP. Furthermore, the mean duration (days) of first admission and chlorpromazine equivalent dosage(mg) in 1 year after first treatment were compared intwopatients groups. Group a DUP > 5 months, Group B < 5 months.

Results  The mean DUP was 13.7 months and the median was 5.0 months. The length of stay of first admission: group A: 121.1 days, and group B: 40.7 days (P=0.018). Chlorpromazine equivalent dosage in 1 year were 770.5 mg in group A, and 226.1 mg in group B (P=0.080).

Discussion  Correlation of DUP and GAF, length of first admission, and chlorpromazine dosage will be discussed.
Subtyping depression by clinical features:the Australasian database
Authors: Parker G. , Roy K. , Hadzi‐Pavlovic D. , Mitchell P. , Wilhelm K. , Menkes D.B. , Snowdon J. , Loo C. , Schweitzer I.
Published: October 2010

Objective: To distinguish psychotic, melancholic and a residual non‐melancholic class on the basis of clinical features alone. Previous studies at our Mood Disorders Unit (MDU) favour a hierarchical model, with the classes able to be distinguished by two specific clinical features, but any such intramural study risks rater bias and requires external replication. Method: This replication study involved 27 Australasian psychiatrist raters, thus extending the sample and raters beyond the MDU facility. They collected clinical feature data using a standardized assessment with precoded rating options. A psychotic depression (PD) class was derived by respecting DSM‐IV decision rules while a cluster analysis distinguished melancholic (MEL) and non‐melancholic classes. Results: The MELs were distinguished virtually entirely by the presence of significant psychomotor disturbance (PMD), as rated by the observationally based CORE measure, with over‐representation on only three of an extensive set of ‘endogeneity symptoms’. Conclusion: In comparison to PMD, endogeneity symptoms appear to be poor indicators of ‘melancholic’ type, confounding typology with severity. Results again support the hierarchical model.
Generalized anxiety disorder (ICD‐10) in primary care from a cross‐cultural perspective: a valid diagnostic entity?
Authors: Maier W. , Gänsicke M. , Freyberger H. J. , Linz M. , Heun R. , Lecrubier Y.
Published: October 2010

Objective:Generalized anxiety disorder (GAD) is a common psychiatric disorder. The nosological status of this diagnostic entity was critically discussed because of the very high rate of comorbidity with other psychiatric disorders, the assumed low degree of social disability associated with GAD in the absence of other disorders, and an ambigious definition.

Method:We explored the frequency and associated social disability of GAD, and examined whether the ICD‐10 definition of GAD is appropriate. The analysis was based on the WHO study on ‘Psychological Problems in Primary Care’ conducted in a standardized manner in 14 countries.

Results:We found GAD (total and without another psychiatric disorder) to be common in primary care in nearly all countries (mean 1‐month prevalence rate, 7.9%), with 25% of these cases presenting with GAD in the absence of any comorbid psychiatric disorder. GAD in general, as well as non‐comorbid GAD, are associated with social disability which is as severe as that in chronic somatic diseases.

Conclusion:It remains questionable whether the current ICD‐10 diagnosis of GAD defining 6 months as a minimum duration and requiring at least four associated symptoms for diagnosis is the most appropriate option. Using this definition, a substantial proportion of psychosocially disabled subjects characterized by anxiety, tension and worrying remain undetected, and are possibly therefore not adequately treated.
One man's meat is another man's poison
Authors: Wardle Jane , Cooke Lucy J
Published: October 2010

Why does one person like cucumber while another hates it? Understanding the causes of our innate and idiosyncratic food preferences has real implications for encouraging children and adults to eat a healthy diet.
Toward a complete model of radial growth in Pinus edulis: the effects of CO2 and prior years
Authors: Tysor C. Susannah , Whipple Amy , Koch George
Published: October 2010

Pinus edulis (piñon pine) is found across 35% of the Colorado Plateau and is a foundation species in the piñon-juniper woodlands of the Southwest. Piñon pine mortality in the recent drought has been high and climate change models forecast a warmer future for the region, which will increase piñon pine water stress. In order to predict the fate of piñon pine, we must understand how various climatic factors influence piñon growth. Tree rings provide a climate sensitive record of growth ideal for exploring the relationship between growth and climate. We used 78 piñon pine trees cored at Red Mountain in northern Arizona in 1998 to predict tree ring width and piñon pine mortality, using variables including available moisture, growing season length, tree age, growth in prior years, and [CO~2~] in a hierarchical Bayes modeling structure. As a first step towards the full model, tree ring width in the prior year and [CO~2~] was considered in a lag 1 year autoregressive model of mean yearly ring width with [CO~2~] as a linear covariate.As a linear covariate, [CO~2~] is related to tree ring width with slope 0.019 (95% Credible Interval (CI) 0.015 to 0.024) and intercept -5.5 (95% CI -6.88 to -4.07). Tree ring width increases with [CO~2~] and [CO~2~] explains the overall increasing trend in average yearly ring width better than available moisture (as Palmer Drought Severity Index values) or growing season length (as the number of days/year with an average of 5°C or higher). The autocorrelation coefficient is 0.49 (95% CI 0.30 to 0.68), suggesting a strong effect of growth in the prior year on growth in the subsequent year. The model successfully predicts yearly average ring width, though ring width is overestimated in extremely dry years. As other factors and more data are incorporated into the model, ring width predictions should improve along with our understanding of piñon growth. We plan to consider the ramifications of various climate change scenarios for piñon pine with this model and compare the responses of trees that have survived to those that have died in the recent drought. As recent experiments indicate that piñon pine mortality can arise from drought-induced carbon starvation, the contribution of increasing [CO~2~] to growth could be very important to predicting piñon pine survival.
Modeling forest insect population dynamics
Authors: Pineda-Krch Mario
Published: October 2010

Overview of the Special Interdisciplinary Minisymposium at the 2009 meeting of the Society for Mathematical Biology on modeling of forest insect population dynamics.
Extracting conclusion sections from PubMed abstracts for rapid key assertion integration in biomedical research
Authors: Samwald Matthias
Published: October 2010

Key assertions are extracted from “conclusions” sections of PubMed abstracts andconverted into Semantic Web / Linked Data format. The results are made accessible viafiles, a SPARQL endpoint, and a faceted search interface. Conclusion sections areidentified as valuable resources for machine-augmented key assertion identification andintegration in the biomedical domain. Results are discussed and opportunities for futurework and cooperation are highlighted.
BRAGOMAP - a new Perl script for high throughoutput blast results analysis including GO and MapMan automatic annotations
Authors: Woycicki Rafal , Gutman Wojciech , Przybecki Zbigniew
Published: October 2010

Analyzing of sequences similarities is the first and most important method used to find out the function of unknown nucleotides. Searching of homologs should be done carefully not to loose any important ones. Having thousands of results from various long-read sequencing projects (ie. differentially expressed tags, genomic polymorphons or BAC ends), the by-hand ability to retrieve interesting (to our goal) similarities in hundreds of Blast results decreases rapidly. Decreasing the number of retrieved sequences by giving more stringency in e-value threshold or displaying less results could lead to false deductions. Functional genomics, proteomics and metabolomics could give us answers to the role of nucleotide sequences. It makes the need to annotate as much of the homologies as we can, to proper molecular function, biological process and cellular component (as its proposed by widely accepted Gene Ontology Consortium annotations or MapMan mappings by Max-Planc-Institute).To facilitate fast retrieval of interesting Blast homologies and making right deductions about the biological role of sequences, in big sequencing projects, the new Perl script BRAGOMAP was written. The program make use of some of BioPerl modules as well as the power of regex text-mining in the Perl itself.The script gives us the possibility to find interesting sequence similarities by using keywords and giving points for each one found. It collects all important information from the GenBank data and puts it in different columns of tab-delimited file for further use. If we were interested (for example) in flower differentiation genes we could use the keywords (flower, ovule, anther, etc.) and/or filter all the homologies isolated from flower tissues in a special development stage. We can also filter results by choosing similarities to interesting genes or protein products. This script retrieve also all standard information from the Blast and GenBank files as Description, ACC no., E-value, Similarity positions, Query Length, Percent of Similarity etc. Automatic GO and MapMan annotations are done by looking for genes, protein products and /or DB references in the proper mappings files. Here we present the usefulness of the script in analyzing sequence similarities and annotations mapping of 3855 BAC ends obtained from the HindIII BAC genomic library of cucumber (Cucumis sativus L., line B10).
Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico
Authors: Spirov Alexander , Holloway David
Published: October 2010

A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests.
A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions
Authors: Gu Jin
Published: October 2010

Transcription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true motifs when noise is high and shows higher specificity for predicting the tissue-specific functions of CRRs.
Standard operating procedures (SOP) in experimental stroke research: SOP for middle cerebral artery occlusion in the mouse
Authors: Dirnagl Ulrich , Group Members of the MCAO-SOP
Published: October 2010

Recently, systematic reviews have found quantitative evidence that low study quality may have introduced a bias into preclinical stroke research. Monitoring, auditing, and standard operating procedures (SOPs) are already key elements of quality control in randomized clinical trials and will hopefully be widely adopted by preclinical stroke research in the near future. Increasingly, funding bodies and review boards overseeing animal experiments are taking a proactive stance, and demand auditable quality control measures in preclinical research. Every good quality control system is based on its SOPs. This article introduces the concept of quality control and presents for the first time an SOP in experimental stroke research.
A new approach to generating research-quality phenology data: The USA National Phenology Monitoring System
Authors: Denny Ellen , Miller-Rushing Abraham , Haggerty Brian , Wilson Bruce , Weltzin Jake , USA-NPN Protocol Development Team the rest of the
Published: October 2010

The USA National Phenology Network (www.usanpn.org) has recently initiated a national effort to encourage people at different levels of expertise—from backyard naturalists to professional scientists—to observe phenology and contribute to a national database that will be used to greatly improve our understanding of spatio-temporal variation in phenology and associated phenological responses to climate change. Many phenological observation protocols identify specific single dates at which individual phenological events are observed, but the scientific usefulness of long-term phenological observations can be improved with a more carefully structured protocol. At the USA-NPN we have developed a new approach that directs observers to record each day that they observe an individual plant, and to assess and report the state of specific life stages (or phenophases) as occurring or not occurring on that plant for each observation date. Observations of animal phenophases are similarly recorded, although for a species as a whole rather than for a specific individual. Evaluation is phrased in terms of simple, easy-to-understand, questions (e.g. “Do you see open flowers?”) which makes it appropriate for a broad audience. From this method, a rich dataset of phenological metrics can be extracted, including the duration of a phenophase (e.g. open flowers), the beginning and end points of a phenophase (e.g. traditional phenological events such as first flower and end flowering), multiple distinct occurrences of phenophases within a single growing season (e.g multiple flowering events, common in drought-prone regions), as well as quantification of sampling frequency and observational uncertainties. The system also includes a mechanism for translation of phenophase start and end points into standard traditional phenological events to facilitate comparison of contemporary data collected with this new “phenophase status” monitoring approach to historical datasets collected with the “phenological event” monitoring approach. These features greatly enhance the utility of the resulting data for statistical analyses addressing questions such as how phenological events vary in time and space, and in response to global change.
Crinumin, a novel substitute of chymotrypsin, may control pancreatic insufficiency and inflammation: Purification and characterization
Authors: Singh Kunwar Awaneesh , Singh Chandan , Rao G.R.K. , Jagannatham M.V.
Published: October 2010

Crinumin, a glycosylated serine protease with chymotrypsin like catalytic specificity was purified from a medicinally important plant Crinum asiaticum of family Amaryllidaceae. Ethno-botanical information and Pharmacological studies confirming about the presence of active bio- molecules in the Crinum played crucial role in injury, inflamed joint, local pain and arthritis. Biomedical research suggests chymotrypsin was not only used as digestive aid but also helpful in the above disease. These findings support towards the crinumin may be the active bio-molecule. Crinumin shows activity over a wide range of pH (4.5-11.5 and optimum at 8.5), temperature (75 °C and optimum at 70 °C) and is also functional against chaotrophs, organic solvents, and detergents even after prolonged exposure. The molecular mass (67.7kDa), extinction coefficient (17.7) and isoelectric point (6.9) were also estimated. The denatured natural substrates, such as casein, azocasein, azoalbumin and haemoglobin were hydrolysed by crinumin with very high specific activity. The enzyme also showed amidolytic activity against synthetic substrates, N-succinyl-Phe-p-nitroanilide and α-leucine-pnitroanilide. The apparent Km, Vmax and Kcat values obtained from the Lineweaver–Burk plot were 5 × 104 μM, 0.316 μM/min and 0.73 with N-succinyl-L-phenylalanine-p-nitroanilide as substrate. The proteolytic activity of the enzyme is inhibited by PMSF but not by SBTI make it more special and useful than other serine proteases being used in the food industry. Easy and economic purification with high yield (33%), stability and activity in adverse conditions with chymotrypsin like functioning make it better among known chymotrypsin enzymes from different sources.
Nuisance Signal in Resting-State fMRI Study
Authors: Zuo Xi-Nian , Milham Michael
Published: October 2010

We systematically presented various nuisance signals in resting-state fMRI (R-fMRI) dataset. First, we examined the impact of different extraction methods on the default-mode pattern seeded by posterior cingulate cortex (PCC). Second, we compared their differences in test-retest reliability. Finally, we speculated the equivalence of removing global mean signal to removing gray matter mean signal.
Precise Atomic Structures of Three Novel Nanomaterials in Nanotechnology, Biomedicine and Cosmology: Graphene, Boron Nitride and Coronene
Authors: Heyrovska Raji , Atchison Lakshmi , Narayan Sara
Published: October 2010

Nanomaterials are currently of great importance in science, technology and commercial applications. Since these materials are atomic layer thick and are a few square nanometers of area, a knowledge of their precise atomic structures will help in the exact understanding of the properties at the nanoscale and in the fabrication and design of the nanomaterials for their many uses. Their known inter-atomic distances have been used here to obtain the exact atomic radii of the component atoms and thereby their precise atomic structures, for the first time. Considered here are three nanomaterials with hexagonal structures, but of quite different properties, namely, graphene (an electrical conductor), boron nitride (an insulator) and coronene (indicators of life in the Universe).
A Unified Approach for Representing Structurally-Complex Models in SBML Level 3
Authors: Muetzelfeldt Robert
Published: October 2010

The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page (http://sbml.org/Community/Wiki/SBML_Level_3_Proposals) which deal with model structure, namely comp, arrays, spatial, geom, dyn and multi. For each one, I consider how the requirements which motivated the package can be handled using Simile's unified approach. Although Simile has a declarative model-representation language (in both Prolog and XML syntax), I use Simile diagrams and equation syntax throughout, since this is more compact and readable than large chunks of XML.The conclusion is that Simile can indeed meet most of the requirements of these various packages, using a generic set of constructs - basically, the multiple-instance submodel, the concept of a relationship (association) between submodels, and array variables. This suggests the possibility of having a single SBML Level 3 extension package similar to the Simile data model, rather than a series of separate packages. Such an approach has a number of potential advantages and disadvantages compared with having the current set of discrete packages: these are discussed in this paper.
Gas phase carbon acidity and correlations with aqueous pK~a~ values: A comparison of B3LYP/6-311++G(d,p), Gaussian-4 (G4), and experimental approaches
Authors: Rayne Sierra , Forest Kaya
Published: October 2010

Gas phase standard state (298.15 K, 1 atm) calculations were conducted at the B3LYP/6-311++G(d,p) density functional and the Gaussian-4 (G4) composite method levels of theory to estimate the acidity of various carbon acids. Excellent agreement was found between the G4 gas phase enthalpies and free energies of carbon acid dissociation and corresponding experimental values. The B3LYP/6-311++G(d,p) level of theory displayed a significantly lower accuracy for gas phase acidity prediction, but with similar qualitative trends as the G4 calculations. Good correlations using both theoretical methods were found with corresponding carbon acid aqueous pK~a~ values. However, the pK~a~ prediction accuracy of carbon acids based on correlations with theoretical gas phase acidities appears lower than previously reported. Some carbon acid moieties may be outliers in general aqueous pK~a~ versus gas phase acidity quantitative structure-property relationships (QSPRs), warranting further investigative efforts on broader training sets.
Genetic vehicle comprising majority of lowly expressed genes guides cell fate decision
Authors: Tsuchiya Masa , Piras Vincent , Tomita Masaru , Giuliani Alessandro , Selvarajoo Kumar
Published: October 2010

Cells remarkably take a specific differentiation path among the multiple possibilities that can arise through the multi-dimensional regulation of genome activities. Such deterministic processes suggest the existence of cellular attractors. However, the origins and drivers of the attractors still remain elusive. Here we analyzed the temporal neutrophil differentiation microarray data for two different stimuli, dimethyl sulfoxide (DMSO) and all-trans-retinoic acid (atRA), and expressed their collective dynamics by temporal Pearson correlation and mutual information coordinates. We constructed ensemble of the genes which showed reduction of correlation fluctuations following the inverse square root law. Evaluating their temporal probability density distributions resulted in the emergence of distinct high density localizations from non-localized low density spread distributions, forming attractor cores for both atRA and DMSO. These attractor cores overlapped, pointing to the existence of a neutrophil cell fate attractor. Notably, we found the localizations of correlation distributions for the majority of lowly expressed genes (LEGs) ensembles overlapped with the whole genome attractor cores, while the remaining genomes’ localizations did not overlap. Therefore, we postulate the existence of genetic vehicle, made up mainly of LEGs, for the guidance of cell fate.
Creating and improving detoxification pathways for interpretation of toxicogenomics data
Authors: Giesbertz Pieter , Hummel Jonas , Gaj Stan , Jennen Danyel , Kelder Thomas , Evelo Chris , van Delft Joost , Kleinjans Jos
Published: October 2010

Current high-throughput technology in genomics creates a large amount of biological data. Bioinformatics approaches are directed towards understanding such data on a systems biology level. Advanced mathematical methods like principal component analysis, clustering, neural networks, support vector machine (SVM) approaches and neural networks can help to find patterns in the data. However, to really understand the data the patterns must be combined with existing knowledge. One of the approaches to do so is to associate these data to functional classifications such as can be found in the Gene Ontology. Other methods focus on using biological pathways coming from both public and private pathway databases like KEGG, WikiPathways, Reactome, and MetaCore. Some of these pathway databases contain rather aspecific information about which genes are involved in reactions. A single identifier, like an Enzyme Code, may correspond to a full family of enzymes, whereas only one family member is responsible for the reaction in the given biological context. Another problem arises in the availability of relevant biological pathways for both rodents and humans. This is especially true in the field of toxicology, where many pathways are still lacking. The focus of this project was to create phase I and phase II detoxification pathways using PathVisio, the pathway editor of WikiPathways. New pathway content was generated using information obtained from several trusted resources: a) handbooks, b) manual/automated PubMed literature searches; c) online pathway resources; d) UniProt Knowledgebase; e) EnsEMBL; f) GeneCards. In addition, the content of some existing toxicology pathways was improved. To illustrate the usefulness of the new pathways data from experiments with carcinogenic compounds were retrieved from the main online microarray data repositories Gene Expression Omnibus (GEO) and ArrayExpress. The resulting data were visualized on the new pathways using PathVisio. All these pathways are made available to the community at WikiPathways, where they can be further used for statistical pathway analysis and visualization in the (toxico)genomics field.