BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation

<p>Abstract</p> <p>Background</p> <p>Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence database searching and operon analysis. Other methods can support these techniques: We have developed an automatic method "BrEPS" that creates highly specific sequence patterns for the functional annotation of enzymes.</p> <p>Results</p> <p>The enzymes in the UniprotKB are identified and their sequences compared against each other with BLAST. The enzymes are then clustered into a number of trees, where each tree node is associated with a set of EC-numbers. The enzyme sequences in the tree nodes are aligned with ClustalW. The conserved columns of the resulting multiple alignments are used to construct sequence patterns. In the last step, we verify the quality of the patterns by computing their specificity. Patterns with low specificity are omitted and recomputed further down in the tree. The final high-quality patterns can be used for functional annotation. We ran our protocol on a recent Swiss-Prot release and show statistics, as well as a comparison to PRIAM, a probabilistic method that is also specialized on the functional annotation of enzymes. We determine the amount of true positive annotations for five common microorganisms with data from BRENDA and AMENDA serving as standard of truth. BrEPS is almost on par with PRIAM, a fact which we discuss in the context of five manually investigated cases.</p> <p>Conclusions</p> <p>Our protocol computes highly specific sequence patterns that can be used to support the functional annotation of enzymes. The main advantages of our method are that it is automatic and unsupervised, and quite fast once the patterns are evaluated. The results show that BrEPS can be a valuable addition to the reconstruction of metabolic networks.</p

Public Continuum Beliefs for Different Levels of Depression Severity

Introduction: The notion that depression is a disorder that moves along a continuum is well-established. Similarly, the belief in the continuity of mental illness is considered an important element in the stigma process. Against this background, it is the aim of this study to examine whether public continuum beliefs vary with the severity of depressive symptoms. Methods: Analyses were based on computer-assisted telephone interviews (CATIs) conducted in winter 2019/2020 in Germany (N = 1,009, response rate 46.8%). Using three vignettes representing mild, moderate, and severe depressive symptoms, beliefs regarding the continuity of symptoms, specifically a fundamental difference, were assessed with seven items. Sociodemographic characteristics and own experiences with depression (affliction and contact) were introduced as covariates. Results: Significant differences between the three groups of severity were found for the majority of the items measuring continuum beliefs or perceived fundamental difference. However, only few items showed a linear trend indicating a parallel between symptom severity and beliefs. Multivariate regression models showed that a moderate degree of depression was positively associated with stronger continuum beliefs but also with greater perceived difference compared to the mild degree, while no significant associations emerged for the severe vignette. Limitations: Although a comparison of our sample with official statistics supports the external validity, we cannot rule out a selection bias. It is arguable in how far short case vignettes convey a holistic picture of a person affected by depressive symptoms. Conclusion: Our results do not indicate a parallel between symptom severity and public continuum beliefs

Bowl Shaped Cavitands Dimerize and Complex Certain Organic Guests in Organic Solvents which Themselves are Poor Guests

The syntheses and binding properties of rigidly bowl-shaped polycyclic cavitands (1—4) are reported. Attached to the four aryl rim positions of the bowls are four benzenes substituted in their para positions with four CC^Me, Br, OH or NO2 groups, which deepen the bowls. Attached to the base of the bowls are four pentyl feet, which increase the solubilities of these hosts in organic solvents. Of the four hosts, only the one containing the CO2Me groups dimerized both in the crystalline state and in solution in ten deute- rated solvents which themselves are poor guests. In three other deuterated solvents, no dimerization was observed. A crystal structure of the dimer showed that one p-MeC^CCs^ group of each monomer occupied the cavity of its complexing partner in a reciprocating double host-guest arrangement. Such a structure is compatible with the ^H-NMR spectra of the dimer in solution. The dimer was also detected in its FAB-MS. The tetrabromocavitand at low concentrations in CD2CI2 complexed MeCC^C^Me, MeCC^Me, PhCC^Me and MeCOC^CC^Me. Tetranitrocavitand 4 also complexed MeC02CH2Me in CD2CI2 as solvent

Intact priors for gaze direction in adults with high-functioning autism spectrum conditions

This research was supported by the UK Medical Research Council under project code MC-A060-5PQ50 (Andrew J. Calder). IM was supported by a Leverhulme Trust Project Grant. CC was supported by an Australian Research Council Future Fellowship. SBC was supported by the MRC, the Wellcome Trust and the Autism Research Trust during the period of this work. The research was also supported by the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care East of England at Cambridgeshire and Peterborough NHS Foundation Trust

Brain lateralization probed by water diffusion at atomic-to-micrometric scale

Combined neutron scattering and diffusion nuclear magnetic resonance experiments have been used to reveal significant interregional asymmetries (lateralization) in bovine brain hemispheres in terms of myelin arrangement and water dynamics at micron to atomic scales. Thicker myelin sheaths were found in the left hemisphere using neutron diffraction. 4.7\u2009T dMRI and quasi-elastic neutron experiments highlighted significant differences in the properties of water dynamics in the two hemispheres. The results were interpreted in terms of hemisphere-dependent cellular composition (number of neurons, cell distribution, etc.) as well as specificity of neurological functions (such as preferential networking)

Validação do zoneamento ecológico do Estado do Paraná para produção de sementes de soja.

Em determinadas regiões do Estado do Paraná, o baixo potencial de germinação, atribuído às condições climáticas desfavoráveis, durante o período de maturação da soja, é o principal fator de eliminação de lotes de sementes. Objetivando avaliar a dimensão do problema o estudo visou determinar as regiões mais apta do Paraná para produção de sementes de soja de elevado padrão fisiológico. Para tal, foram coletadas 121 amostras de sementes da cultivar BR16 (1996/97, 1997/98 e 1998/1999) e 119 amostras da cultivar BRS 133 (1999/2000, 2000/2001 e 20012002). Os parâmetros tomados por base para analisar a qualidade das sementes foram: germinação (%), vigor (TZ 1-3), viabilidade (TZ 1-5), deterioração por umidade (TZ 6-8), dano mecânico (6-8) e lesões de percevejos (TZ 6-8). Para interpretação dos dados, o estado do Paraná foi dividido em três regiões ecológicas: T1, temperatura média do mês mais quente (Fevereiro) >24oC; T2, temperatura média entre 22 e 24oC; T3, temperatura média <22oC. A região T3 que abrange os municípios de Ponta Grossa, Guarapuava, Pato Branco, Marilândia do Sul, Francisco Beltrão e parte de Cascavel, destacou-se, invariavelmente, por apresentar reduzidos índices de sementes com deterioração por umidade, com dano mecânico e com lesões de percevejos, resultando num melhor potencial de germinação, de vigor e de viabilidade. A validação do zoneamento ecológico adiciona uma tecnologia capaz de identificar a região Sul do estado do Paraná, com melhores condições climáticas para produção de sementes de soja de qualidade

Public Continuum Beliefs for Different Levels of Depression Severity

Introduction: The notion that depression is a disorder that moves along a continuum is well-established. Similarly, the belief in the continuity of mental illness is considered an important element in the stigma process. Against this background, it is the aim of this study to examine whether public continuum beliefs vary with the severity of depressive symptoms.Methods: Analyses were based on computer-assisted telephone interviews (CATIs) conducted in winter 2019/2020 in Germany (N = 1,009, response rate 46.8%). Using three vignettes representing mild, moderate, and severe depressive symptoms, beliefs regarding the continuity of symptoms, specifically a fundamental difference, were assessed with seven items. Sociodemographic characteristics and own experiences with depression (affliction and contact) were introduced as covariates.Results: Significant differences between the three groups of severity were found for the majority of the items measuring continuum beliefs or perceived fundamental difference. However, only few items showed a linear trend indicating a parallel between symptom severity and beliefs. Multivariate regression models showed that a moderate degree of depression was positively associated with stronger continuum beliefs but also with greater perceived difference compared to the mild degree, while no significant associations emerged for the severe vignette.Limitations: Although a comparison of our sample with official statistics supports the external validity, we cannot rule out a selection bias. It is arguable in how far short case vignettes convey a holistic picture of a person affected by depressive symptoms.Conclusion: Our results do not indicate a parallel between symptom severity and public continuum beliefs

Public Beliefs About Somatic Symptom Disorders

Objectives: Despite satisfactory effectiveness of treatment for somatic symptom disorders (SSD), treatment rates are low and treatment is usually initiated many years after first symptoms. In order to understand whether a lack of public mental health literacy might contribute to these poor treatment rates, we aimed to focus on two research questions: (1) What does the German public know and think about SSD? (2) Are knowledge and beliefs associated with socio-demographic factors and experiences with the disorder?Methods: Two vignettes with symptoms of a SSD were used in a national telephone survey in Germany (N = 1,004). Vignettes differed regarding main type of symptom (pain vs. fatigue) and existence of an earlier somatic disease (yes vs. no). Respondents were asked concerning knowledge and beliefs about causes, symptoms, and treatment using a standardized questionnaire.Results: 66% of the respondents agreed that a possible cause of the symptoms is a misinterpretation of body signals. About 1/3 recognized a mental health problem when confronted with the vignettes of cases with SSD. This rate was lower in case of a SSD with pain as the main symptom without a comorbid somatic disease (24.8%, 95%-CI: 21.1–28.6) compared to a case with fatigue as the main symptom and an earlier severe somatic disease (44.0%, 95%-CI: 39.6–48.3). Female respondents tended to have a more positive view on treatability and effectiveness of psychotherapy, while associations of knowledge and beliefs with education and age were inconsistent. Respondents who had contact with a person with SSD were more likely to think that psychotherapy is effective and that they know a lot about SSD compared to those who never had contact.Conclusions: While most of the German public seems to be well informed about causes of SSD as well as treatability and the effectiveness of psychotherapy, the majority has problems with interpreting symptoms and does not think they know a lot about symptoms like that. Increasing knowledge about SSD by education interventions may help to promote adequate help seeking