Reciprocal recombination genomic signatures in the symbiotic arbuscular mycorrhizal fungi Rhizophagus irregularis.

Arbuscular mycorrhizal fungi (AMF) are part of the most widespread fungal-plant symbiosis. They colonize at least 80% of plant species, promote plant growth and plant diversity. These fungi are multinucleated and contain either one or two haploid nuclear genotypes (monokaryon and dikaryon) identified by the alleles at a putative mating-type locus. This taxon has been considered as an ancient asexual scandal because of the lack of observable sexual structures. Despite identification of a putative mating-type locus and functional activation of genes related to mating when two isolates co-exist, it remains unknown if the AMF life cycle involves a sexual or parasexual stage. We used publicly available genome sequences to test if Rhizophagus irregularis dikaryon genomes display signatures of sexual reproduction in the form of reciprocal recombination patterns, or if they display exclusively signatures of parasexual reproduction involving gene conversion. We used short-read and long-read sequence data to identify nucleus-specific alleles within dikaryons and then compared them to orthologous gene sequences from related monokaryon isolates displaying the same putative MAT-types as the dikaryon. We observed that the two nucleus-specific alleles of the dikaryon A5 are more related to the homolog sequences of monokaryon isolates displaying the same putative MAT-type than between each other. We also observed that these nucleus-specific alleles displayed reciprocal recombination signatures. These results confirm that dikaryon and monokaryon isolates displaying the same putative MAT-type are related in their life-cycle. These results suggest that a genetic exchange mechanism, involving reciprocal recombination in dikaryon genomes, allows AMF to generate genetic diversity.

Computer-assisted initial diagnosis of rare diseases.

Introduction. Most documented rare diseases have genetic origin. Because of their low individual frequency, an initial diagnosis based on phenotypic symptoms is not always easy, as practitioners might never have been exposed to patients suffering from the relevant disease. It is thus important to develop tools that facilitate symptom-based initial diagnosis of rare diseases by clinicians. In this work we aimed at developing a computational approach to aid in that initial diagnosis. We also aimed at implementing this approach in a user friendly web prototype. We call this tool Rare Disease Discovery. Finally, we also aimed at testing the performance of the prototype. Methods. Rare Disease Discovery uses the publicly available ORPHANET data set of association between rare diseases and their symptoms to automatically predict the most likely rare diseases based on a patient's symptoms. We apply the method to retrospectively diagnose a cohort of 187 rare disease patients with confirmed diagnosis. Subsequently we test the precision, sensitivity, and global performance of the system under different scenarios by running large scale Monte Carlo simulations. All settings account for situations where absent and/or unrelated symptoms are considered in the diagnosis. Results. We find that this expert system has high diagnostic precision (≥80%) and sensitivity (≥99%), and is robust to both absent and unrelated symptoms. Discussion. The Rare Disease Discovery prediction engine appears to provide a fast and robust method for initial assisted differential diagnosis of rare diseases. We coupled this engine with a user-friendly web interface and it can be freely accessed at http://disease-discovery.udl.cat/. The code and most current database for the whole project can be downloaded from https://github.com/Wrrzag/DiseaseDiscovery/tree/no_classifiers.

CheNER: a tool for the identification of chemical entities and their classes in biomedical literature.

BACKGROUND: Small chemical molecules regulate biological processes at the molecular level. Those molecules are often involved in causing or treating pathological states. Automatically identifying such molecules in biomedical text is difficult due to both, the diverse morphology of chemical names and the alternative types of nomenclature that are simultaneously used to describe them. To address these issues, the last BioCreAtIvE challenge proposed a CHEMDNER task, which is a Named Entity Recognition (NER) challenge that aims at labelling different types of chemical names in biomedical text. METHODS: To address this challenge we tested various approaches to recognizing chemical entities in biomedical documents. These approaches range from linear Conditional Random Fields (CRFs) to a combination of CRFs with regular expression and dictionary matching, followed by a post-processing step to tag those chemical names in a corpus of Medline abstracts. We named our best performing systems CheNER. RESULTS: We evaluate the performance of the various approaches using the F-score statistics. Higher F-scores indicate better performance. The highest F-score we obtain in identifying unique chemical entities is 72.88%. The highest F-score we obtain in identifying all chemical entities is 73.07%. We also evaluate the F-Score of combining our system with ChemSpot, and find an increase from 72.88% to 73.83%. CONCLUSIONS: CheNER presents a valid alternative for automated annotation of chemical entities in biomedical documents. In addition, CheNER may be used to derive new features to train newer methods for tagging chemical entities. CheNER can be downloaded from http://metres.udl.cat and included in text annotation pipelines.

Bilateral ophthalmic artery occlusion.

We describe an unusual case of an elderly patient with all the symptoms of ocular ischaemic syndrome and stenosis of both ophthalmic arteries alone.

[Epidural lipomatosis secondary to corticotherapy]. / Lipomatose epidural secundária a corticoterapia.

Spinal epidural lipomatosis is the excessive deposition of unencapsulated fat in the epidural space. This is a rare disorder often associated with high levels of endogenous steroids or the administration of exogenous steroids. A precocious diagnosis is important because it influences the clinical evolution and the therapeutics option. The computed tomography (CT) and magnetic resonance imaging (MRI) are very important to the diagnosis. Authors report a case of a mediastinal and epidural lipomatosis in a man receiving corticoid therapy, with symptoms consistent with acute respiratory failure and progressive paraparesis.

Intracranial aneurysm and vasculopathy after surgery and radiation therapy for craniopharyngioma: case report.

OBJECTIVE AND IMPORTANCE: This case report illustrates the possible occurrence of intracranial aneurysms after surgery and radiation-induced vasculopathy. CLINICAL PRESENTATION: An internal carotid bifurcation aneurysm was diagnosed in a 19-year-old woman in a routine follow-up examination by magnetic resonance imaging 5 years after subtotal removal of a giant cystic craniopharyngioma treated by postoperative external radiotherapy. The presence of the aneurysm was confirmed by angiography. INTERVENTION: It was decided to treat the aneurysm by embolization with Guglielmi detachable coiling. However, at the beginning of the procedure, a few weeks after the diagnosis, a dramatic reduction in the carotid artery blood flow was observed, along with signs of thrombosis inside the aneurysm. In light of these findings, the procedure was aborted. Four months later, another angiographic examination confirmed the exclusion of the aneurysm and compensatory flow through the external carotid artery. CONCLUSION: During the assessment of patients who have undergone postoperative radiotherapy, the potential for the development of aneurysms and radiation-induced vasculopathy exists and should be kept in mind. Considering the potential for spontaneous thrombosis of these aneurysms, cautious judgment is recommended before making a decision to treat them.