Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae

Principles and guidelines are presented to ensure a solid scientific standard of papers dealing with the taxonomy of taxa of Pasteurellaceae Pohl 1981. The classification of the Pasteurellaceae is in principle based on a polyphasic approach. DNA sequencing of certain genes is very important for defining the borders of a taxon. However, the characteristics that are common to all members of the taxon and which might be helpful for separating it from related taxa must also be identified. Descriptions have to be based on as many strains as possible (inclusion of at least five strains is highly desirable), representing different sources with respect to geography and ecology, to allow proper characterization both phenotypically and genotypically, to establish the extent of diversity of the cluster to be named. A genus must be monophyletic based on 16S rRNA gene sequence-based phylogenetic analysis. Only in very rare cases is it acceptable that monophyly can not be achieved by 16S rRNA gene sequence comparison. Recently, the monophyly of genera has been confirmed by sequence comparison of housekeeping genes. In principle, a new genus should be recognized by a distinct phenotype, and characters that separate the new genus from its neighbours should be given clearly. Due to the overall importance of accurate classification of species, at least two genotypic methods are needed to show coherence and for separation at the species level. The main criterion for the classification of a novel species is that it forms a monophyletic group based on 16S rRNA gene sequence-based phylogenetic analysis. However, some groups might also include closely related species. In these cases, more sensitive tools for genetic recognition of species should be applied, such as DNA-DNA hybridizations. The comparison of housekeeping gene sequences has recently been used for genotypic definition of species. In order to separate species, phenotypic characters must also be identified to recognize them, and at least two phenotypic differences from existing species should be identified if possible. We recommend the use of the subspecies category only for subgroups associated with disease or similar biological characteristics. At the subspecies level, the genotypic groups must always be nested within the boundaries of an existing species. Phenotypic cohesion must be documented at the subspecies level and separation between subspecies and related species must be fully documented, as well as association with particular disease and host. An overview of methods previously used to characterize isolates of the Pasteurellaceae has been given. Genotypic and phenotypic methods are separated in relation to tests for investigating diversity and cohesion and to separate taxa at the level of genus as well as species and subspecies.

An Experience-Driven Pedagogy for the Instruction of Software Testing in Computer Science

In the realm of computer programming, the experience of writing a program is used to reinforce concepts and evaluate ability. This research uses three case studies to evaluate the introduction of testing through Kolb's Experiential Learning Model (ELM). We then analyze the impact of those testing experiences to determine methods for improving future courses. The first testing experience that students encounter are unit test reports in their early courses. This course demonstrates that automating and improving feedback can provide more ELM iterations. The JUnit Generation (JUG) tool also provided a positive experience for the instructor by reducing the overall workload. Later, undergraduate and graduate students have the opportunity to work together in a multi-role Human-Computer Interaction (HCI) course. The interactions use usability analysis techniques with graduate students as usability experts and undergraduate students as design engineers. Students get experience testing the user experience of their product prototypes using methods varying from heuristic analysis to user testing. From this course, we learned the importance of the instructors role in the ELM. As more roles were added to the HCI course, a desire arose to provide more complete, quality assured software. This inspired the addition of unit testing experiences to the course. However, we learned that significant preparations must be made to apply the ELM when students are resistant. The research presented through these courses was driven by the recognition of a need for testing in a Computer Science curriculum. Our understanding of the ELM suggests the need for student experience when being introduced to testing concepts. We learned that experiential learning, when appropriately implemented, can provide benefits to the Computer Science classroom. When examined together, these course-based research projects provided insight into building strong testing practices into a curriculum.

Congenital retinal macrovessels: description of three cases and review of the literature

BACKGROUND: Congenital retinal macrovessels are large aberrant branches of retinal arteries or veins that cross the macula. We present three patients with a unilateral congenital retinal macrovessel and we conduct a review of the literature. PATIENTS AND METHODS: A 22-year-old man complaining of chronic headache as well as two other men, 18 and 23 years old, respectively, during a routine ophthalmological examination, were found with a unilateral congenital retinal macrovessel each. A thorough ophthalmological examination was performed, including colour fundus photography in all three patients and fluorescein angiography in two of the patients. We followed them up for five years. THERAPY AND OUTCOME: Investigation revealed a unilateral venous congenital retinal macrovessel in all patients. Clinical findings and visual acuity remained unchanged throughout the entire follow-up period. No complications were recorded. CONCLUSIONS: Congenital retinal macrovessels are rare and they tend to remain stable. Visual acuity is preserved in most cases. Complications occur only occasionally and have been described in the literature. Differential diagnosis from other arteriovenous malformations affecting multiple organs is necessary.

Severe autoimmune cytopenias in treatment-naive hepatitis C virus infection: clinical description of 16 cases

OBJECTIVE: To describe the prevalence, main characteristics, and treatment of severe autoimmune cytopenias [autoimmune hemolytic anemia (AIHA), autoimmune thrombocytopenic purpura (AITP)] in patients with chronic hepatitis C virus (HCV) infection. METHODS: Retrospective chart review of patients with chronic HCV infection seen at our institution. Two additional departments contributed eight more patients to assess therapy of HCV-related autoimmune cytopenias. RESULTS: Eight patients (seven AITP, one AIHA) fulfilled the inclusion criteria in our population of 4345 HCV-infected patients. The number of patients with AITP was much greater than would be expected by chance (P<0.0001). Patients with HCV-related AITP were older and demonstrated more immunological markers than a group of 40 controls. Eight additional patients (six AITP, two Evans syndrome) were included. We only assessed the response for AITP patients because of the single case of AIHA. Patients with AITP had a poor response to initial corticosteroids [one complete response (CR), three partial response (PR), and four failures]. Intravenous immunoglobulins led to transient efficacy in three of four patients. In second-line therapy, five of seven patients responded to splenectomy. Rituximab proved effective in increasing platelets in two patients. Of eight patients treated with antiviral therapy (IFN-alpha+/-ribavirin), five responded (three CR, two PR). CONCLUSION: AITP occurs more commonly in patients with chronic HCV infection than would be expected by chance. HCV-positive AITP requires a treatment strategy different from that used in HCV-negative AITP. On the basis of the results from our study and a literature analysis, we propose an algorithm for treatment of severe HCV-related autoimmune cytopenias.

Contrast-enhanced MR myelography in spontaneous intracranial hypotension: description of an artefact imitating CSF leakage

In contrast-enhanced (CE) MR myelography, hyperintense signal outside the intrathecal space in T1-weighted sequences with spectral presaturation inversion recovery (SPIR) is usually considered to be due to CSF leakage. We retrospectively investigated a hyperintense signal at the apex of the lung appearing in this sequence in patients with SIH (n = 5), CSF rhinorrhoea (n = 2), lumbar spine surgery (n = 1) and in control subjects (n = 6). Intrathecal application of contrast agent was performed in all patients before MR examination, but not in the control group. The reproducible signal increase was investigated with other fat suppression techniques and MR spectroscopy. All patients and controls showed strongly hyperintense signal at the apex of the lungs imitating CSF leakage into paraspinal tissue. This signal increase was identified as an artefact, caused by spectroscopically proven shift and broadening of water and lipid resonances (1-2 ppm) in this anatomical region. Only patients with SIH showed additional focal enhancement along the spinal nerve roots and/or in the spinal epidural space. In conclusion CE MR myelography with spectral selective fat suppression shows a reproducible cervicothoracic artefact, imitating CSF leakage. Selective water excitation technique as well as periradicular and epidural contrast collections may be helpful to discriminate between real pathological findings and artefacts.

Automatic Labeling of Software Components and their Evolution using Log-Likelihood Ratio of Word Frequencies in Source Code

As more and more open-source software components become available on the internet we need automatic ways to label and compare them. For example, a developer who searches for reusable software must be able to quickly gain an understanding of retrieved components. This understanding cannot be gained at the level of source code due to the semantic gap between source code and the domain model. In this paper we present a lexical approach that uses the log-likelihood ratios of word frequencies to automatically provide labels for software components. We present a prototype implementation of our labeling/comparison algorithm and provide examples of its application. In particular, we apply the approach to detect trends in the evolution of a software system.

Classification of the taxon 2 and taxon 3 complex of Bisgaard within Gallibacterium and description of Gallibacterium melopsittaci sp. nov., Gallibacterium trehalosifermentans sp. nov. and Gallibacterium salpingitidis sp. nov

This investigation was based on 23 isolates from several European countries collected over the past 30 years, and included characterization of all isolates. Published data on amplified fragment length polymorphism typing of isolates representing all biovars as well as protein profiles were used to select strains that were then further characterized by polyamine profiling and sequencing of 16S rRNA, infB, rpoB and recN genes. Comparison of 16S rRNA gene sequences revealed a monophyletic group within the avian 16S rRNA group of the Pasteurellaceae, which currently includes the genera Avibacterium, Gallibacterium and Volucribacter. Five monophyletic subgroups related to Gallibacterium anatis were recognized by 16S rRNA, rpoB, infB and recN gene sequence comparisons. Whole-genome similarity between strains of the five subgroups and the type strain of G. anatis calculated from recN sequences allowed us to classify them within the genus Gallibacterium. In addition, phenotypic data including biochemical traits, protein profiling and polyamine patterns clearly indicated that these taxa are related. Major phenotypic diversity was observed for 16S rRNA gene sequence groups. Furthermore, comparison of whole-genome similarities, phenotypic data and published data on amplified fragment length polymorphism and protein profiling revealed that each of the five groups present unique properties that allow the proposal of three novel species of Gallibacterium, for which we propose the names Gallibacterium melopsittaci sp. nov. (type strain F450(T) =CCUG 36331(T) =CCM 7538(T)), Gallibacterium trehalosifermentans sp. nov. (type strain 52/S3/90(T) =CCUG 55631(T) =CCM 7539(T)) and Gallibacterium salpingitidis sp. nov. (type strain F150(T) =CCUG 15564(T) =CCUG 36325(T) =NCTC 11414(T)), a novel genomospecies 3 of Gallibacterium and an unnamed taxon (group V). An emended description of the genus Gallibacterium is also presented.