Search

BackgroundMexico's 2009 "narcomenudeo reform" decriminalized small amounts of drugs, shifting some drug law enforcement to the states and mandating drug treatment diversion instead of incarceration. Data from Tijuana suggested limited implementation of this harm reduction-oriented policy. We studied whether a police education program (PEP) improved officers' drug and syringe policy knowledge, and aimed to identify participant characteristics associated with improvement of drug policy knowledge.MethodsPre- and post-training surveys were self-administered by municipal police officers to measure legal knowledge. Training impact was assessed through matched paired nominal data using McNemar's tests. Multivariable logistic regression was used to identify predictors of improved legal knowledge, as measured by officers' ability to identify conceptual legal provisions related to syringe possession and thresholds of drugs covered under the reform.ResultsOf 1750 respondents comparing pre- versus post training, officers reported significant improvement (p

A structure-based approach to the design of protein ligands was developed, based on the transfer of a functional binding motif of amino acids on a host protein able to reproduce the functional topology of the residues. The results of the experiment showed that protein ligands have binding results consistent with the presumed binding mode.

Objetivo. Establecer si ciertas características de los jóvenes influyen en la elección de las personas con quienes hablan sobre el SIDA. Material y métodos. A partir de una encuesta realizada por el Consejo Nacional para la Prevención y Control del SIDA (CONASIDA) en 1997 se hizo una regresión logística multinomial. El estudio abarca a 4 886 jóvenes de uno u otro sexo, de 15 a 19 años, en 13 entidades federativas de México. Resultados. El modelo, que incluye las variables sexo, actividad sexual, condición de actividad laboral y escolaridad del padre resultó significativo y altamente predictor de las personas con quienes los jóvenes hablan del SIDA, siempre en comparación con los jóvenes que no hablan con nadie. Los hombres jóvenes hablan del SIDA con su padre más que las mujeres, y las mujeres más con su madre. Los sexualmente activos hablan más con los amigos, y algo menos con los maestros, que los sexualmente inactivos. A mayor escolaridad del padre, los jóvenes tienen más interlocutores y hablan más sobre el SIDA en el ámbito familiar, comparados con los que tienen padre sin escolaridad. Conclusiones. Se sugiere diseñar estrategias diferenciadas de educación en salud sexual de acuerdo con las características de las subpoblaciones.

RNA-binding proteins (RBPs) are key regulators of gene expression. Here, we introduce EuPRI (Eukaryotic Protein-RNA Interactions) - a freely available resource of RNA motifs for 34,736 RBPs from 690 eukaryotes. EuPRI includes in vitro binding data for 504 RBPs, including newly collected RNAcompete data for 174 RBPs, along with thousands of reconstructed motifs. We reconstruct these motifs with a new computational platform - Joint Protein-Ligand Embedding (JPLE) - which can detect distant homology relationships and map specificity-determining peptides. EuPRI quadruples the number of known RBP motifs, expanding the motif repertoire across all major eukaryotic clades, and assigning motifs to the majority of human RBPs. EuPRI drastically improves knowledge of RBP motifs in flowering plants. For example, it increases the number of Arabidopsis thaliana RBP motifs 7-fold, from 14 to 105. EuPRI also has broad utility for inferring post-transcriptional function and evolutionary relationships. We demonstrate this by predicting a role for 12 Arabidopsis thaliana RBPs in RNA stability and identifying rapid and recent evolution of post-transcriptional regulatory networks in worms and plants. In contrast, the vertebrate RNA motif set has remained relatively stable after its drastic expansion between the metazoan and vertebrate ancestors. EuPRI represents a powerful resource for the study of gene regulation across eukaryotes., Competing Interests: Declaration of interests The authors declare no competing interests.

Many fields of biology rely on the inference of accurate multiple sequence alignments (MSA) of biological sequences. Unfortunately, the problem of assembling an MSA is NP-complete thus limiting computation to approximate solutions using heuristics solutions. The progressive algorithm is one of the most popular frameworks for the computation of MSAs. It involves pre-clustering the sequences and aligning them starting with the most similar ones. The scalability of this framework is limited, especially with respect to accuracy. We present here an alternative approach named regressive algorithm. In this framework, sequences are first clustered and then aligned starting with the most distantly related ones. This approach has been shown to greatly improve accuracy during scale-up, especially on datasets featuring 10,000 sequences or more. Another benefit is the possibility to integrate third-party clustering methods and third-party MSA aligners. The regressive algorithm has been tested on up to 1.5 million sequences, its implementation is available in the T-Coffee package.

Multiple sequence alignments (MSAs) are used for structural 1,2 and evolutionary predictions 1,2 , but the complexity of aligning large datasets requires the use of approximate solutions 3 , including the progressive algorithm 4 . Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf to root, based on a guide tree. Their accuracy declines substantially as the number of sequences is scaled up 5 . We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around from the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes 6 .

Sex work around the world takes place under conditions of structural violence and vulnerability. The México-U.S. border region is characterized by the presence of factors that increase the risk for health harms among female sex workers (FSW); located in this context, the risk environments of Tijuana and Ciudad Juárez have similar yet distinct characteristics that influence how risk is produced and experienced among FSWs. Exploring the ways in which FSWs enact agency in risk environments can illustrate how environmental characteristics shape perceived risks and the strategies that FSWs develop to manage them. This approach also identifies the limits that are placed by environmental characteristics over the capacity for harm reduction and prevention practices among FSWs. We analyzed the role of agency in the work environments of female sex workers and its relationship with risk perception and management in the cities of Tijuana and Cd. Juárez., Competing Interests: Disclosure statement No potential conflict of interest was reported by the authors.

Objective: To measure HPV vaccine acceptance in diverse Mexican adult popula-tions, taking into account HIV status., Materials and Methods: A total of 1 329 men and women, with and without HIV, participated in one of three intervention studies, offering HPV vaccination, carried out in the states of Morelos, Tlaxcala and Mexico City; either the bivalent (Morelos n=103, Tlaxcala n=127) or quadrivalent HPV-vaccine (Mexico City n=1 099) was offered., Results: HPV vaccine was accepted by 80.3% of participants; acceptance was higher in people living with HIV than those without (84.4 vs. 78%, p=0.004). Women had greater HPV infection knowledge (p<0.0001) than men and slightly higher (p=0.4) vaccine acceptance. The main reason for vaccine non-acceptance among HIV-positive participants was their doctor recommended they not get vaccinated., Conclusions: Acceptance of HPV-vaccine was high in men and women regardless of HIV status. Even higher rates of acceptability may be achieved by educating healthcare providers to recommend HPV vaccine to their patients., Competing Interests: Declaration of conflict of interests. The authors declare that they have no conflict of interests.

Objective: To evaluate the effectiveness of a combined strategy of human papillomavirus virus (HPV) vaccination and high-risk HPV screening to reduce the occurrence of anogenital and oropharyngeal neoplasms among men who have sex with men, people with HIV, homeless people, transgender women, female sex workers and rape victims., Materials and Methods: This mixed methods study evaluates the effectiveness of a combined vaccination-screening strategy to reduce HPV prevalence/incidence and occurrence of cervical intraepithelial neoplasms grade 2+ and/or anal intraepithelial neoplasms grade 2+, using Kaplan-Meier. The time-to-event method will evaluate time from positive results for specific anogenital HPV to incidence of anogenital lesions containing that HPV type., Results: People vaccinated against HPV and screened for HPV as a primary test will have lower prevalence and incidence of HPV infection and consequently lower frequency of HPV-related anogenital and oropharyngeal lesions., Conclusions: Thisstudy will generate scientific evidence on effectiveness of a combined vaccination-screening strategy to reduce the burden of HPV-associated neoplasms., Competing Interests: Declaration of conflict of interests. The authors declare that they have no conflict of interests.

Reproducing routine bioinformatics analysis is challenging owing to a combination of factors hard to control for. Nextflow is a flow management framework that uses container technology to insure efficient deployment and reproducibility of computational analysis pipelines. Third party pipelines can be ported into Nextflow with minimum re-coding. We used RNA-Seq quantification, genome annotation and phylogeny reconstruction examples to show how two seemingly irreproducible analyzes can be made stable across platforms when ported into Nextflow., (© Société de Biologie, 2018.)

This review provides an overview on the development of Multiple sequence alignment (MSA) methods and their main applications. It is focused on progress made over the past decade. The three first sections review recent algorithmic developments for protein, RNA/DNA and genomic alignments. The fourth section deals with benchmarks and explores the relationship between empirical and simulated data, along with the impact on method developments. The last part of the review gives an overview on available MSA local reliability estimators and their dependence on various algorithmic properties of available methods., (© The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.)

The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)

T-Coffee, for Tree-based consistency objective function for alignment evaluation, is a versatile multiple sequence alignment (MSA) method suitable for aligning virtually any type of biological sequences. T-Coffee provides more than a simple sequence aligner; rather it is a framework in which alternative alignment methods and/or extra information (i.e., structural, evolutionary, or experimental information) can be combined to reach more accurate and more meaningful MSAs. T-Coffee can be used either by running input data via the Web server ( http://tcoffee.crg.cat/apps/tcoffee/index.html ) or by downloading the T-Coffee package. Here, we present how the package can be used in its command line mode to carry out the most common tasks and multiply align proteins, DNA, and RNA sequences. This chapter particularly emphasizes on the description of T-Coffee special flavors also called "modes," designed to address particular biological problems.

This article introduces the T-RMSD web server (tree-based on root-mean-square deviation), a service allowing the online computation of structure-based protein classification. It has been developed to address the relation between structural and functional similarity in proteins, and it allows a fine-grained structural clustering of a given protein family or group of structurally related proteins using distance RMSD (dRMSD) variations. These distances are computed between all pairs of equivalent residues, as defined by the ungapped columns within a given multiple sequence alignment. Using these generated distance matrices (one per equivalent position), T-RMSD produces a structural tree with support values for each cluster node, reminiscent of bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology. The clusters thus defined have been shown to be structurally and functionally informative. The T-RMSD web server is a free website open to all users and available at http://tcoffee.crg.cat/apps/tcoffee/do:trmsd.

Tumor Necrosis Factor Ligand (TNFL)-Tumor Necrosis Factor Receptor (TNFR) interactions control key cellular processes; however, the molecular basis of the specificity of these interactions remains poorly understood. Using the T-RMSD (tree based on root mean square deviation), a newly developed structure-based sequence clustering method, we have re-analyzed the available structural data to re-interpret the interactions between TNFLs and TNFRs. This improves the classification of both TNFLs and TNFRs, such that the new groups defined here are in much stronger agreement with structural and functional features than existing schemes. Our clustering approach also identifies traces of a convergent evolutionary process for TNFLs and TNFRs, leading us to propose the co-evolution of TNFLs and the third cysteine rich domain (CRD) of large TNFRs., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

T-Coffee (Tree-based consistency objective function for alignment evaluation) is a versatile multiple sequence alignment (MSA) method suitable for aligning most types of biological sequences. The main strength of T-Coffee is its ability to combine third party aligners and to integrate structural (or homology) information when building MSAs. The series of protocols presented here show how the package can be used to multiply align proteins, RNA and DNA sequences. The protein section shows how users can select the most suitable T-Coffee mode for their data set. Detailed protocols include T-Coffee, the default mode, M-Coffee, a meta version able to combine several third party aligners into one, PSI (position-specific iterated)-Coffee, the homology extended mode suitable for remote homologs and Expresso, the structure-based multiple aligner. We then also show how the T-RMSD (tree based on root mean square deviation) option can be used to produce a functionally informative structure-based clustering. RNA alignment procedures are described for using R-Coffee, a mode able to use predicted RNA secondary structures when aligning RNA sequences. DNA alignments are illustrated with Pro-Coffee, a multiple aligner specific of promoter regions. We also present some of the many reformatting utilities bundled with T-Coffee. The package is an open-source freeware available from http://www.tcoffee.org/.

Objective: This article aims to examine data on Psychiatric diagnoses among deaf people in comparison with hearing people in the psychiatric hospital in Beau-Vallon., Method: This work proposes to study the diagnostic data from the Summary Psychiatric Minimum (Résumé psychiatrique minimum: RPM) from the years 2000 until 2009 from the psychiatric hospital Beau Vallon and for which a hearing problem has been highlighted on Axis III. The sample data of the deaf population will be compared with the sample of the total population represented by all patients for the year 2008. Both samples were found to be equivalent after a Mann-Whitney test to study the relationship between two independent samples with quantitative data., Results: The results show an overrepresentation of the diagnosis of psychotic disorders (40.7% against 29.3%), an equivalence of depressive disorders (18.5% against 18%) but bipolar disorders were absent in the deaf while they were found in 5.7% of patients with normal hearing, an overrepresentation in the deaf population of anxiety disorders (11.1% against 3.4%), intellectual disabilities (37% against 13.4% in the hearing population) and an under-representation of personality disorders (25.9% against 61.2% in the hearing population), Conclusion: In this example, several concepts can be put forward to demonstrate bias and prejudice in the specific diagnostic support for deaf people with psychiatric teams who are not specialized in the treatment of deafness.

This study addresses the relation between structural and functional similarity in proteins. We introduce a novel method named tree based on root mean square deviation (T-RMSD), which uses distance RMSD (dRMSD) variations to build fine-grained structure-based classifications of proteins. The main improvement of the T-RMSD over similar methods, such as Dali, is its capacity to produce the equivalent of a bootstrap value for each cluster node. We validated our approach on two domain families studied extensively for their role in many biological and pathological pathways: the small GTPase RAS superfamily and the cysteine-rich domains (CRDs) associated with the tumor necrosis factor receptors (TNFRs) family. Our analysis showed that T-RMSD is able to automatically recover and refine existing classifications. In the case of the small GTPase ARF subfamily, T-RMSD can distinguish GTP- from GDP-bound states, while in the case of CRDs it can identify two new subgroups associated with well defined functional features (ligand binding and formation of ligand pre-assembly complex). We show how hidden Markov models (HMMs) can be built on these new groups and propose a methodology to use these models simultaneously in order to do fine-grained functional genomic annotation without known 3D structures. T-RMSD, an open source freeware incorporated in the T-Coffee package, is available online., (2010 Elsevier Ltd. All rights reserved.)

The incidence of Mycobacterium malmoense infections compared to other non-tuberculous mycobacteria (NTM) has increased since 1980, especially in northern Europe. Based on various epidemiological and clinical reports outside northern Europe, there is a wide distribution of these infections. Infections with M. malmoense cause pulmonary disease comparable with tuberculosis (TB). The main extra-pulmonary disease type is paediatric cervical lymphadenitis. M. malmoense isolates are clinically significant in about 70-80% of patients. Like other NTM infections, M. malmoense is often found in patients with chronic obstructive pulmonary disease (COPD) and may cause serious morbidity and mortality when inadequately treated. The best treatment consists of a 2-year regimen with rifampicin and ethambutol. The literature on infections with M. malmoense is reviewed with respect to epidemiology, clinical presentation, treatment and outcome.

Objective: To analyze the social construction of stigma and discrimination processes associated with HIV/AIDS and people living with HIV/AIDS (PLHA), based on the perceptions of health care providers in three states of the Mexican Republic., Material and Methods: Qualitative and quantitative description. Observation at nine institutions; in-depth interviews (14) and surveys (373) directed to providers of health services., Results: Seventy-five percent of providers reported having received training related to HIV/AIDS; however, notions persist as to patients being hopeless; discrimination due to the idea of risk groups; the immediate identification of living with the virus, having the syndrome and death; and specific lack of knowledge of forms of transmission. Twenty-three percent would not buy food from a PLHA and 16% think they should be banned from public services. With respect to confidentiality: 89% believe it should be maintained and 38% think that employers and administrators have the right to know about their employees' condition. Isolation, notes in clinical histories pointing to HIV, obligatory testing and delays in surgeries for PLHA were constant practices. The perception that men who have sexual relations with men and sexual workers decide their sexual practices marks the division between innocent victims and guilty ones, which determines the stigmatization and discrimination processes in health services., Conclusions: The design of strategies to decrease stigma and discrimination associated with HIV/AIDS demands the inclusion of an ethical debate about human rights and a structural focus regarding social conditions that go beyond the notion of risk behaviors.

Injection drug use is a growing problem on the US-Mexico border, where Tijuana is situated. We studied the context of injection drug use among injection drug users (IDUs) in Tijuana to help guide future research and interventions. Guided in-depth interviews were conducted with 10 male and 10 female current IDUs in Tijuana. Topics included types of drug used, injection settings, access to sterile needles, and environmental influences. Interviews were taped, transcribed verbatim, and translated. Content analysis was conducted to identify themes. Of the 20 IDUs, median age and age at first injection were 30 and 18. Most reported injecting at least daily: heroin ("carga", "chiva", "negra"), methamphetamine ("crico", "cri-cri"), or both drugs combined. In sharp contrast to Western US cities, almost all regularly attended shooting galleries ("yongos" or "picaderos") because of the difficulties obtaining syringes and police oppression. Almost all shared needles/paraphernalia ["cuete" (syringe), "cacharros" (cookers), cotton from sweaters/socks (filters)]. Some reported obtaining syringes from the United States. Key themes included (1) pharmacies refusing to sell or charging higher prices to IDUs, (2) ample availability of used/rented syringes from "picaderos" (e.g., charging approximately 5 pesos or "10 drops" of drug), and (3) poor HIV/AIDS knowledge, such as beliefs that exposing syringes to air "kills germs." This qualitative study suggests that IDUs in Tijuana are at high risk of HIV and other blood-borne infections. Interventions are urgently needed to expand access to sterile injection equipment and offset the potential for a widespread HIV epidemic.

Objective: To investigate the current sexual behavior and condom use during the first sexual intercourse among adolescents, as well as variations and factors influencing condom use at first sexual intercourse., Material and Methods: The data source for this study was Mexico's National Health Survey 2000. Study subjects were male and female adolescents aged 12 to 19 years (n = 16,258). Statistical analysis consisted of descriptive statistics and multivariate logistic regression, to assess the association of four types of factors (demographic, socioeconomic, cultural, and cognitive) with condom use during the first sexual intercourse., Results: Males and residents of urban areas reported greater sexual activity and condom use. Typically, adolescents who used condoms during the first sexual intercourse were male, older, resided in urban areas, non-speakers of an indigenous language, and with higher schooling., Conclusions: New policies should be framed to prevent sexually transmitted infections to span the gap between knowledge and practice, targeting adolescents starting sexual activity earlier, those who speak an indigenous language, living in rural areas, with less schooling, and females. The English version of this paper is available too at:http://www.insp.mx/salud/index.html.

Objective: The objective of this article is to provide a comprehensive overview of the evolution of the Mexican HIV/AIDS surveillance system between 1986 and 2001., Design: All information was collected through an extensive literature search., Methods: Databases such as the Mexican National AIDS Programmes RIMSIDA (Registry of Mexican AIDS Research), MedLINE, PopLine, and AIDSLINE were used. Databases, keywords, and MeSH headings to search were discussed and agreed upon before and during the literature search., Results: Two hundred and twenty articles and conference abstracts were reviewed and showed that the Mexican surveillance system has undergone many adaptations. The HIV/AIDS surveillance system began in 1986, when the focus was on identifying AIDS cases. This period was followed by special studies among risk groups, and served as the basis for the sentinel surveillance system that was adopted in 1990. The system now requires HIV and AIDS case reporting as well as sentinel surveillance. Mexico has also carried out the piloting of the behavioural surveillance component of Second Generation Surveillance., Conclusion: The Mexican experience illustrates how surveillance systems need to be dynamic in order to monitor trends in HIV over time. This review also demonstrates that middle-income countries can successfully implement surveillance systems. However, although Mexico has had many successes, a need exists to address issues that limit its ability to implement AIDS case and behavioural surveillance fully and consistently.

Objective: To establish whether certain characteristics of the young influence their choice of people with whom to discuss AIDS., Material and Methods: A national survey was conducted in 1997 by the Consejo Nacional para la Prevención y Control del SIDA (CONASIDA, Mexican Council for AIDS Prevention and Control). Study subjects were 4886 male and female 15-19 year-old teenagers. Multinomial logistic regression was used to analyze data., Results: A model including the variables sex, sexual activity, work conditions, and father's schooling level, turned out to be significant and highly predictive of people with whom teenagers discuss AIDS, as compared to teenagers speaking with no one. Male teenagers discuss AIDS with their fathers more than female teenagers, and female teenagers discuss AIDS more with their mothers. Sexually active teenagers discuss AIDS more with their friends and less with their teachers than sexually inactive teenagers. The greater schooling level the father has, the more people teenagers have with whom to discuss AIDS and the more they discuss AIDS at home, compared to teenagers with fathers without schooling., Conclusions: Differentiated sexual education training strategies should be designed in accordance with subpopulations' characteristics. The English version of this paper is available at: http://www.insp.mx/salud/index.html.