Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes.

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 binding data for 504 RBPs, including newly collected RNAcompete data for 174 RBPs, along with thousands of reconstructed motifs.

Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation.

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.

Large multiple sequence alignments with a root-to-leaf regressive method.

Multiple sequence alignments (MSAs) are used for structural and evolutionary predictions, but the complexity of aligning large datasets requires the use of approximate solutions, including the progressive algorithm. 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.

Women in Sex Work and the Risk Environment: Agency, Risk Perception, and Management in the Sex Work Environments of Two Mexico-U.S. Border Cities.

Sex work around the world takes place under conditions of structural violence and vulnerability. The México-U.S.

Prevention and control of neoplasms associated with HPV in high-risk groups in Mexico City: The Condesa Study.

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.

HPV vaccine acceptance is high among adults in Mexico, particularly in people living with HIV.

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.

[Nextflow, an efficient tool to improve computation numerical stability in genomic analysis].

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.

Measuring improvement in knowledge of drug policy reforms following a police education program in Tijuana, Mexico.

Background: Mexico'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.

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

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.

Multiple sequence alignment modeling: methods and applications.

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.

T-Coffee: Tree-based consistency objective function for alignment evaluation.

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.

T-RMSD: a web server for automated fine-grained protein structural classification.

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.

An improved understanding of TNFL/TNFR interactions using structure-based classifications.

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.

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.

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 case of the Beau-Vallon": mental illnesses of deaf people to the psychiatric hospital.

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.

T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors.

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.

The rising incidence and clinical relevance of Mycobacterium malmoense: a review of the literature.

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.

Structure-based secondary structure-independent approach to design protein ligands: Application to the design of Kv1.2 potassium channel blockers.

We have developed a structure-based approach to the design of protein ligands. This approach is based on the transfer of a functional binding motif of amino acids, often referred as to the "hot spot", on a host protein able to reproduce the functional topology of these residues. The scaffolds were identified by a systematic in silico search in the Protein Data Bank for proteins possessing a group of residues in a topology similar to that adopted by the functional motif in a reference ligand of known 3D structure.

[HIV/AIDS-related stigma and discrimination: the case of health care providers in México].

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.

"Vivo para consumirla y la consumo para vivir" ["I live to inject and inject to live"]: high-risk injection behaviors in Tijuana, Mexico.

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.

[Use of condoms among Mexican adolescents for the prevention of sexually transmitted diseases].

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).

The Mexican HIV/AIDS surveillance system: 1986-2001.

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.

[Whom do Mexican adolescents talk to about AIDS?].

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.