HAMAP in 2015: updates to the protein family classification and annotation system.

HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorithm.

A variant in the gene FUT9 is associated with susceptibility to placental malaria infection

Malaria in pregnancy forms a substantial part of the worldwide burden of malaria, with an estimated annual death toll of up to 200,000 infants, as well as increased maternal morbidity and mortality. Studies of genetic susceptibility to malaria have so far focused on infant malaria, with only a few studies investigating the genetic basis of placental malaria, focusing only on a limited number of candidate genes. The aim of this study therefore was to identify novel host genetic factors involved in placental malaria infection. To this end we carried out a nested case-control study on 180 Mozambican pregnant women with placental malaria infection, and 180 controls within an intervention trial of malaria prevention. We genotyped 880 SNPs in a set of 64 functionally related genes involved in glycosylation and innate immunity. A SNP located in the gene FUT9, rs3811070, was significantly associated with placental malaria infection (OR = 2.31, permutation p-value = 0.028). Haplotypic analysis revealed a similarly strong association of a common haplotype of four SNPs including rs3811070. FUT9 codes for a fucosyl-transferase that is catalyzing the last step in the biosynthesis of the Lewis-x antigen, which forms part of the Lewis blood group-related antigens. These results therefore suggest an involvement of this antigen in the pathogenesis of placental malaria infection.

Avancées thérapeutiques dans les epilepsies réfractaires de l'enfant [Therapeutic advances in refractory epilepsies in children].

Epilepsy concerns several thousands of children in Switzerland, and is refractory to classic antiepileptic drugs in an important proportion of cases. This percentage has remained stable, despite a constant production of new antiepileptic molecules. To alleviate this problem, several alternative approaches have been developed these last years. In this article, we present three children who suffer from different forms of pharmacoresistant epilepsy, managed with immunomodulatory or neurosurgical treatments, and we summarize the current knowledge about these therapeutic options.

The street and children’s informal economy in Cape Verde

Since the 1990s Cape Verde has undergone dramatic economic and political transformations that have brought about growing social class distinction. The two main towns (Praia and Mindelo) have grown rapidly in the last decades and their urban structure today reflects the increasing polarisation of the population. Middle and upper class families occupy the older parts of town and the recently built planned areas, while spontaneous neighbourhoods spread without planning on the less valuable land. It is in these latter areas that most social issues associated with childhood and youth have become highly visible in the last decade. In this article I will focus on children’s reasons for going to live on the streets of Mindelo, arguing that it is in terms of autonomous mobility within a non-heterogeneous and profoundly divided urban and social space that we can better understand what is commonly defined as the phenomenon of street children.

Limited clinical benefit of minority K103N and Y181C-variant detection in addition to routine genotypic resistance testing in antiretroviral therapy-naive patients.

OBJECTIVE: The presence of minority nonnucleoside reverse transcriptase inhibitor (NNRTI)-resistant HIV-1 variants prior to antiretroviral therapy (ART) has been linked to virologic failure in treatment-naive patients. DESIGN: We performed a large retrospective study to determine the number of treatment failures that could have been prevented by implementing minority drug-resistant HIV-1 variant analyses in ART-naïve patients in whom no NNRTI resistance mutations were detected by routine resistance testing. METHODS: Of 1608 patients in the Swiss HIV Cohort Study, who have initiated first-line ART with two nucleoside reverse transcriptase inhibitors (NRTIs) and one NNRTI before July 2008, 519 patients were eligible by means of HIV-1 subtype, viral load and sample availability. Key NNRTI drug resistance mutations K103N and Y181C were measured by allele-specific PCR in 208 of 519 randomly chosen patients. RESULTS: Minority K103N and Y181C drug resistance mutations were detected in five out of 190 (2.6%) and 10 out of 201 (5%) patients, respectively. Focusing on 183 patients for whom virologic success or failure could be examined, virologic failure occurred in seven out of 183 (3.8%) patients; minority K103N and/or Y181C variants were present prior to ART initiation in only two of those patients. The NNRTI-containing, first-line ART was effective in 10 patients with preexisting minority NNRTI-resistant HIV-1 variant. CONCLUSION: As revealed in settings of case-control studies, minority NNRTI-resistant HIV-1 variants can have an impact on ART. However, the implementation of minority NNRTI-resistant HIV-1 variant analysis in addition to genotypic resistance testing (GRT) cannot be recommended in routine clinical settings. Additional associated risk factors need to be discovered.

Update on skin cancer incidence and mortality in Europe

The epidemiology of skin cancer shows interplay between host susceptibility, (ultraviolet) environment, socioeconomical conditions and behavioural patterns. Its etiology is not yet fully elucidated and reveals intriguing questions. Fair-skinned populations have experienced over the last 60 years a rapid increase in the incidence of melanoma which is unparalleled by any other cancer, although signs of levelling off and stabilization in incidence have recently been observed in some countries. Despite many primary prevention and early detection campaigns over the last decades in Europe, decreases in melanoma mortality are modest and limited to a few countries. Further, reduction in the incidence of thick melanomas has not yet been evidenced. In this presentation, drivers for the incidence and mortality trends of skin cancer, with a strong focus on melanoma, its most lethal form, will be discussed.

Patterns and trends in esophageal cancer mortality and incidence in Europe (1980-2011) and predictions to 2015

BACKGROUND: Over the last few decades, esophageal cancer incidence and mortality trends varied substantially across Europe, with important differences between sexes and the two main histological subtypes, squamous cell carcinoma (ESCC) and adenocarcinoma (EAC). PATIENTS AND METHODS: To monitor recent esophageal cancer mortality trends and to compute short-term predictions in the European Union (EU) and selected European countries, we analyzed data provided by the World Health Organization (WHO) for 1980-2011. We also analyzed incidence trends and relative weights of ESCC and EAC across Europe using data from Cancer Incidence in Five Continents. RESULTS: Long-term decreasing trends were observed for male esophageal cancer mortality in several southern and western European countries, whereas in central Europe mortality increased until the mid-1990s and started to stabilize or decline over the last years. In some eastern and northern countries, the rates were still increasing. Mortality among European women remained comparatively low and showed stable or decreasing trends in most countries. Between 2000-2004 and 2005-2009, esophageal cancer mortality declined by 7% (from 5.34 to 4.99/100 000) in EU men, and by 3% (from 1.12 to 1.09/100 000) in EU women. Predictions to 2015 show persistent declines in mortality rates for men in the EU overall, and stable rates for EU women, with rates for 2015 of 4.5/100 000 men (about 22 300 deaths) and 1.1/100 000 women (about 7400 deaths). In northern Europe, EAC is now the predominant histological type among men, while for European women ESCC is more common and corresponding rates are still increasing in several countries. CONCLUSION(S): The observed trends reflect the variations in alcohol drinking, tobacco smoking and overweight across European countries.

The referent : a new referential methodology and procedure in live drawing

My research in live drawing and new technologies uses a combination of a human figure in live in composition, overlaid with a digital projection of a second human figure. The aim is to explore, to amplify and thoroughly analyse the search for distinctive identities and graphic languages of representation for live and projected models.

Risque thrombotique sous procréation médicalement assistée [Thrombotic risk in assisted reproductive technology].

Use of assisted reproductive technology (ART) is increasing in many developed countries. Arterial and venous thromboembolic complications are reported during ART with an incidence of 0.1%. The development of these events has been mainly ascribed to the presence of ovarian hyperstimulation syndrome (OHSS). Precise mechanisms by which OHSS and exogenous hormonal stimulation used in ART induce thromboembolic events remain unclear. However, vascular endothelial growth factor secreted during OHSS, high estradiol concentrations, and blood hyperviscosity play a major role in inducing a prothrombotic state. Therefore, before planning an ART, individual thromboembolic risk should be assessed and thromboprophylaxis offered to high risk patients. Prophylaxis should be initiated in women who develop moderate-to-severe OHSS.

The use of the vac in complex wounds - does it work and how?

Background: Complex wounds pose a major challenge in reconstructive and trauma surgery. Several approaches to increase the healing process have been proposed in the last decades. In this study we study the mechanism of action of the Vacuum Assisted Closure device in diabetic wounds. Methods: Full-thickness wounds were excised in diabetic mice and treated with the VAC device or its isolated components: an occlusive dressing (OD) alone, subathmospheric pressure at 125 mm Hg (Suction), and a polyurethane foam without (Foam) and with (Foamc) downward compression of approximately 125 mm Hg. The last goups were treated with either the complete VAC device (VAC) or with a silicne interface that alows fluid removel (Mepithel-VAC). The effects of the treatment modes on the wound surface were quantified by a two-dimensional immunohistochemical staging system based on vasculature, as defined by blood vessel density (CD31) and cell proliferation (defined by ki67 positivity), 7 days post wounding. Finite element modelling was used to predict wound surface deformation under dressing modes and cross sections of in situ fixed tissues were used to measure actual microstrain. Results: The foam-wound interface of the Vacuum Assisted Closure device causes significant wound stains (60%) causing a deformation of the single cell level leading to a profound upregulation of cell proliferation (4-fold) and angiogenisis (2.2-fold) compared to OD treated wounds. Polyurethane foam exposure itself causes a frather unspecific angiogenic response (Foamc, 2 - fold, Foam, 2.2 - fold) without changes of the cell proliferation rate of the wound bed. Suction alone without a specific interface does not have an effect on meassured parameters, showing similar results to untreated wounds. A perforated silicone interface caused a significant lower microdeforamtion of the wound bed correlating to changes of the wound tissues. Conclusion: The Vacuum Assisted Closure device induce significanttissue growth in diabetic wounds. The wound foam interface under suction causes profound macrodeformation that stimulates tissue growth by angiogenesis and cell proliferation. It needs to be taken in consideration that in the clinical setting different wound types may profit from different elements of this suction device.

Systemic and pulmonary vascular dysfunction in children conceived by assisted reproductive technologies.

BACKGROUND: Assisted reproductive technology (ART) involves the manipulation of early embryos at a time when they may be particularly vulnerable to external disturbances. Environmental influences during the embryonic and fetal development influence the individual's susceptibility to cardiovascular disease, raising concerns about the potential consequences of ART on the long-term health of the offspring. METHODS AND RESULTS: We assessed systemic (flow-mediated dilation of the brachial artery, pulse-wave velocity, and carotid intima-media thickness) and pulmonary (pulmonary artery pressure at high altitude by Doppler echocardiography) vascular function in 65 healthy children born after ART and 57 control children. Flow-mediated dilation of the brachial artery was 25% smaller in ART than in control children (6.7±1.6% versus 8.6±1.7%; P<0.0001), whereas endothelium-independent vasodilation was similar in the 2 groups. Carotid-femoral pulse-wave velocity was significantly (P<0.001) faster and carotid intima-media thickness was significantly (P<0.0001) greater in children conceived by ART than in control children. The systolic pulmonary artery pressure at high altitude (3450 m) was 30% higher (P<0.001) in ART than in control children. Vascular function was normal in children conceived naturally during hormonal stimulation of ovulation and in siblings of ART children who were conceived naturally. CONCLUSIONS: Healthy children conceived by ART display generalized vascular dysfunction. This problem does not appear to be related to parental factors but to the ART procedure itself. CLINICAL TRIAL REGISTRATION: URL: www.clinicaltrials.gov. Unique identifier: NCT00837642.

Mitologia i literatura a "Suddenly Last Summer" de Tennessee Williams: tot lluitant contra Venus i Èdip

The aim of this article is to analyze accurately the role played by two classical references, Venus and Oedipus, in Tennessee Williams¿s Suddenly Last Summer, in accordance with the usual nature of studies on Classical Tradition ¿Greek and Roman- and focusing in this case on the relationship between literature and mythology. It is thanks to Venus and Oedipus that the playwright succeeds in showing the magnitude of men¿s and women¿s tragedy, which from his point of view is simply that they have failed to see either kindness in the face of God or to feel his loving and fatherly providence.

Mitología y Literatura en "Suddenly Last Summer" de Tennessee Williams: luchando contra Venus y Edipo

The aim of this article is to analyze accurately the role played by two classical references, Venus and Oedipus, in Tennessee Williams's Suddenly Last Summer, in accordance with the usual nature of studies on Classical Tradition -Greek and Roman- and focusing in this case on the relationship between literature and mythology. It is thanks to Venus and Oedipus that the playwright succeeds in showing the magnitude of men¿s and women¿s tragedy, which from his point of view is simply that they have failed to see either kindness in the face of God or to feel his loving and fatherly providence.

Worldwide trends in gastric cancer mortality (1980-2011), with predictions to 2015, and incidence by subtype.

Gastric cancer incidence and mortality decreased substantially over the last decades in most countries worldwide, with differences in the trends and distribution of the main topographies across regions. To monitor recent mortality trends (1980-2011) and to compute short-term predictions (2015) of gastric cancer mortality in selected countries worldwide, we analysed mortality data provided by the World Health Organization. We also analysed incidence of cardia and non-cardia cancers using data from Cancer Incidence in Five Continents (2003-2007). The joinpoint regression over the most recent calendar periods gave estimated annual percent changes (EAPC) around -3% for the European Union (EU) and major European countries, as well as in Japan and Korea, and around -2% in North America and major Latin American countries. In the United States of America (USA), EU and other major countries worldwide, the EAPC, however, were lower than in previous years. The predictions for 2015 show that a levelling off of rates is expected in the USA and a few other countries. The relative contribution of cardia and non-cardia gastric cancers to the overall number of cases varies widely, with a generally higher proportion of cardia cancers in countries with lower gastric cancer incidence and mortality rates (e.g. the USA, Canada and Denmark). Despite the favourable mortality trends worldwide, in some countries the declines are becoming less marked. There still is the need to control Helicobacter pylori infection and other risk factors, as well as to improve diagnosis and management, to further reduce the burden of gastric cancer.

Metabolic effects of a mixed and a high-carbohydrate low-fat diet in man, measured over 24 h in a respiration chamber.

1. The relation between dietary carbohydrate: lipid ratio and the fuel mixture oxidized during 24 h was investigated in eleven healthy volunteers (six females, and five males) in a respiration chamber. Values of the fuel mixture oxidized were estimated by continuous indirect calorimetry and urinary nitrogen measurements. 2. The subjects, were first given a mixed diet for 7 d and spent the last 24 h of the 7 d period in a respiration chamber for continuous gas-exchange measurement. The fuels oxidized during 2.5 h or moderate exercise were also measured in the respiration chamber. After an interval of 2 weeks from the end of the mixed-diet period, the same subjects were given an isoenergetic high-carbohydrate low-fat diet for 7 d, and the same experimental regimen was repeated. 3. Dietary composition markedly influenced the fuel mixture oxidized during 24 h and this effect was still present 12 h after the last meal in the postabsorptive state. However, the diets had no influence on the substrates oxidized above resting levels during exercise. With both diets, the 24 h energy balance was slightly negative and the energy deficit was covered by lipid oxidation. 4. With the high-carbohydrate low-fat diet, the energy expenditure during sleep was found to be higher than that with the mixed diet. 5. It is concluded that: (a) the composition of the diet did not influence the fuel mixture utilized for moderate exercise, (b) the energy deficit calculated for a 24 h period was compensated by lipid oxidation irrespective of the carbohydrate content of the diet, (c) energy expenditure during sleep was found to be higher with the high-carbohydrate low-fat diet than with the mixed diet.