Predicting protein function by machine learning on amino acid sequences – a critical evaluation

Copyright @ 2007 Al-Shahib et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Predicting the function of newly discovered proteins by simply inspecting their amino acid sequence is one of the major challenges of post-genomic computational biology, especially when done without recourse to experimentation or homology information. Machine learning classifiers are able to discriminate between proteins belonging to different functional classes. Until now, however, it has been unclear if this ability would be transferable to proteins of unknown function, which may show distinct biases compared to experimentally more tractable proteins. Results: Here we show that proteins with known and unknown function do indeed differ significantly. We then show that proteins from different bacterial species also differ to an even larger and very surprising extent, but that functional classifiers nonetheless generalize successfully across species boundaries. We also show that in the case of highly specialized proteomes classifiers from a different, but more conventional, species may in fact outperform the endogenous species-specific classifier. Conclusion: We conclude that there is very good prospect of successfully predicting the function of yet uncharacterized proteins using machine learning classifiers trained on proteins of known function

Creating structure from disorder: using folksonomies to create semantic metadata

This paper reports on an on-going research project to create educational semantic metadata out of folksonomies. The paper describes a simple scenario for the usage of the generated semantic metadata in teaching, and describes the ‘FolksAnnotation’ tool which applies an organization scheme to tags in a specific domain of interest. The contribution of this paper is to describe an evaluation framework which will allow us to validate our claim that folksonomies are potentially a rich source of metadata

Erratum: Erratum to “A 78 Years Old Male With Painful Erythematous Skin Lesions in Lower Extremity”: [International Journal of Infectious Diseases, 2016 48, Pages 32] International Journal of Infectious Diseases 2016 49 170

The publisher regrets that the paper was published without Figures 1, 2 and 3. The publisher would like to apologise for any inconvenience caused

Making if-then plans counteracts learned non-use in stroke patients: A proof-of-principle study

Background: After stroke, the learned non-use of a paretic arm is a major obstacle to the improvement of hand function. / Objective: We examined whether patients with a central paresis could profit from applying the self-regulation strategy of making if-then plans that specify situational triggers to using the paretic arm. / Method: Seventeen stroke patients with a mild to moderate hand paresis were asked to perform a Simon task which is commonly used to study the enhanced executive control needed when there is a mismatch between stimulus (e.g., color) and response (e.g., location) features. We examined whether patients with hemiparesis would be able to reduce the Simon effect (i.e., responding slower to mismatched as compared to matched stimulus and response features) by creating new stimulus-response associations via if-then plans. / Results: A significant Simon effect was observed in both the affected and the non-affected arm for control trials. However, there was no longer a significant Simon effect for the critical trials prepared by forming if-then plans. This led to a significant stimulus×compatibility interaction effect for the affected arm and a marginally significant interaction effect for the nonaffected arm. Making if-then plans was effective for eliminating or at least reducing the Simon effect for the affected and the non-affected arm, respectively. / Conclusion: This observation opens a potential new route to improving stroke rehabilitation. If-then plans may qualify as a viable strategy to overcome the learned non-use of the affected arm. Further research is now required to develop and test therapeutic measures based on this proof-of-principle

AADC deficiency from infancy to adulthood: Symptoms and developmental outcome in an international cohort of 63 patients

Aromatic l-amino acid decarboxylase deficiency (AADCD) is a rare, autosomal recessive neurodevelopmental disorder characterized by impaired synthesis of dopamine, noradrenaline, adrenaline and serotonin, leading to a complex syndrome of motor, behavioral, and autonomic symptoms. This retrospective study assessed the symptoms and developmental outcome of a large international cohort of patients with AADCD via physician and/or caregiver responses to a detailed, standardized questionnaire. Sixty-three patients (60% female; ages 6 months-36 years, median 7 years; 58 living) from 23 individual countries participated. Common symptoms at onset (median age 3 months, range 0-12 months) were hypotonia, developmental delay, and/or oculogyric crises. Oculogyric crises were present in 97% of patients aged 2 to 12 years, occurred in the majority of patients in all age groups, and tended to be most severe during early childhood. Prominent non-motor symptoms were sleep disturbance, irritable mood, and feeding difficulties. The majority of subjects (70%) had profound motor impairment characterized by absent head control and minimal voluntary movement, while 17% had mild motor impairment and were able to walk independently. Dopamine agonists were the medications most likely to produce some symptomatic benefit, but were associated with dose-limiting side effects (dyskinesia, insomnia, irritability, vomiting) that led to discontinuation 25% of the time. The age distribution of our cohort (70% of subjects under age 13 years) and the observation of a greater proportion of patients with a more severe disease phenotype in the younger compared to the older patients, both suggest a significant mortality risk during childhood for patients with severe disease

Acute abdomen caused by bladder rupture attributable to neurogenic bladder dysfunction following a stroke: a case report.

INTRODUCTION: Spontaneous bladder rupture is a rare and serious event with high mortality. It is not often considered in the patient presenting with peritonitis. This often leads to delays in diagnosis. There are very few case reports of true spontaneous rupture in the literature. This is the first such reported case in which bladder rupture was attributable to neurogenic bladder dysfunction following a stroke. CASE PRESENTATION: We report the case of a 67-year-old Caucasian man who presented with lower abdominal pain and a peritonitic abdomen. He had a long-term urethral catheter because of urinary retention following a previous stroke. He was treated conservatively with antibiotics before a surgical opinion was sought. Exploratory laparotomy confirmed the diagnosis of spontaneous bladder rupture. After repair of the defect, he eventually made a full recovery. CONCLUSION: In this unusual case report, we describe an example of a serious event in which delays in diagnosis may lead to increased morbidity and mortality. To date, no unifying theory explaining why rupture occurs has been postulated. We conducted a thorough literature search to examine the etiological factors in other published cases. These etiological factors either increase intra-vesical pressure or decrease the strength of the bladder wall. We hope that by increasing awareness of these etiological factors, spontaneous bladder rupture may be diagnosed earlier and appropriate therapy started