RinA controls phage-mediated packaging and transfer of virulence genes in gram-positive bacteria

Phage-mediated transfer of microbial genetic elements plays a crucial role in bacterial life style and evolution. In this study, we identify the RinA family of phage-encoded proteins as activators required for transcription of the late operon in a large group of temperate staphylococcal phages. RinA binds to a tightly regulated promoter region, situated upstream of the terS gene, that controls expression of the morphogenetic and lysis modules of the phage, activating their transcription. As expected, rinA deletion eliminated formation of functional phage particles and significantly decreased the transfer of phage and pathogenicity island encoded virulence factors. A genetic analysis of the late promoter region showed that a fragment of 272 bp contains both the promoter and the region necessary for activation by RinA. In addition, we demonstrated that RinA is the only phage-encoded protein required for the activation of this promoter region. This region was shown to be divergent among different phages. Consequently, phages with divergent promoter regions carried allelic variants of the RinA protein, which specifically recognize its own promoter sequence. Finally, most Gram-postive bacteria carry bacteriophages encoding RinA homologue proteins. Characterization of several of these proteins demonstrated that control by RinA of the phage-mediated packaging and transfer of virulence factor is a conserved mechanism regulating horizontal gene transfer.

A survey of fingerprint classification Part I: taxonomies on feature extraction methods and learning models

This paper reviews the fingerprint classification literature looking at the problem from a double perspective. We first deal with feature extraction methods, including the different models considered for singular point detection and for orientation map extraction. Then, we focus on the different learning models considered to build the classifiers used to label new fingerprints. Taxonomies and classifications for the feature extraction, singular point detection, orientation extraction and learning methods are presented. A critical view of the existing literature have led us to present a discussion on the existing methods and their drawbacks such as difficulty in their reimplementation, lack of details or major differences in their evaluations procedures. On this account, an experimental analysis of the most relevant methods is carried out in the second part of this paper, and a new method based on their combination is presented.

A survey of fingerprint classification Part II: experimental analysis and ensemble proposal

In the first part of this paper we reviewed the fingerprint classification literature from two different perspectives: the feature extraction and the classifier learning. Aiming at answering the question of which among the reviewed methods would perform better in a real implementation we end up in a discussion which showed the difficulty in answering this question. No previous comparison exists in the literature and comparisons among papers are done with different experimental frameworks. Moreover, the difficulty in implementing published methods was stated due to the lack of details in their description, parameters and the fact that no source code is shared. For this reason, in this paper we will go through a deep experimental study following the proposed double perspective. In order to do so, we have carefully implemented some of the most relevant feature extraction methods according to the explanations found in the corresponding papers and we have tested their performance with different classifiers, including those specific proposals made by the authors. Our aim is to develop an objective experimental study in a common framework, which has not been done before and which can serve as a baseline for future works on the topic. This way, we will not only test their quality, but their reusability by other researchers and will be able to indicate which proposals could be considered for future developments. Furthermore, we will show that combining different feature extraction models in an ensemble can lead to a superior performance, significantly increasing the results obtained by individual models.

Human papillomavirus detection in women with and without human immunodeficiency virus infection in Colombia

Background: HIV infection leads to a decreasing immune response, thereby facilitating the appearance of other infections, one of the most important ones being HPV. However, studies are needed for determining associations between immunodeficiency caused by HIV and/or the presence of HPV during the course of cervical lesions and their degree of malignancy. This study describes the cytological findings revealed by the Papanicolaou test, laboratory characteristics and HPV molecular profile in women with and without HIV infection. Methods: A total of 216 HIV-positive and 1,159 HIV-negative women were invited to participate in the study; PCR was used for the molecular detection of HPV in cervical samples. Statistical analysis (such as percentages, Chi-square test and Fisher's exact test when applicable) determined human papillomavirus (HPV) infection frequency (single and multiple) and the distribution of six types of high-risk-HPV in women with and without HIV infection. Likewise, a logistic regression model was run to evaluate the relationship between HIV-HPV infection and different risk factors. Results: An association was found between the frequency of HPV infection and infection involving 2 or more HPV types (also known as multiple HPV infection) in HIV-positive women (69.0% and 54.2%, respectively); such frequency was greater than that found in HIV-negative women (44.3% and 22.7%, respectively). Statistically significant differences were observed between both groups (p = 0.001) regarding HPV presence (both in infection and multiple HPV infection). HPV-16 was the most prevalent type in the population being studied (p = 0.001); other viral types had variable distribution in both groups (HIV-positive and HIV-negative). HPV detection was associated with <500 cell/mm(3) CD4-count (p = 0.004) and higher HIV-viral-load (p = 0.001). HPV-DNA detection, <200 cell/mm(3) CD4-count (p = 0.001), and higher HIV-viral-load (p = 0.001) were associated with abnormal cytological findings. Conclusions: The HIV-1 positive population in this study had high multiple HPV infection prevalence. The results for this population group also suggested a greater association between HPV-DNA presence and cytological findings. HPV detection, together with low CD4 count, could represent useful tools for identifying HIV-positive women at risk of developing cervical lesions.

Coronica general de la Orden de San Benito, Patriarca de Religiosos

Colofón en v.1, v.2, v.5, v.6, y v.7.