Hepatitis C virus infections in the Swiss HIV Cohort Study: a rapidly evolving epidemic.

BACKGROUND: Hepatitis C virus (HCV) infection has a growing impact on morbidity and mortality in patients infected with human immunodeficiency virus (HIV). We assessed trends in HCV incidence in the different HIV transmission groups in the Swiss HIV Cohort Study (SHCS). METHODS: HCV infection incidence was assessed from 1998, when routine serial HCV screening was introduced in the SHCS, until 2011. All HCV-seronegative patients with at least 1 follow-up serology were included. Incidence rates (IRs) of HCV infections were compared between men who have sex with men (MSM), injection drug users (IDU), and heterosexuals (HET). RESULTS: HCV incidence was assessed in 3333 MSM, 123 IDU, and 3078 HET with a negative HCV serology at baseline. Over 23 707 person-years (py) for MSM, 733 py for IDU, and 20 752 py for HET, 101 (3%), 41 (33%), and 25 (1%) of patients seroconverted, respectively. The IR of HCV infections in MSM increased from 0.23 (95% credible interval [CrI], .08-.54) per 100 py in 1998 to 4.09 (95% CrI, 2.57-6.18) in 2011. The IR decreased in IDU and remained <1 per 100 py in HET. In MSM, history of inconsistent condom use (adjusted hazard ratio [HR], 2.09; 95% CI, 1.33-3.29) and past syphilis (adjusted HR, 2.11; 95% confidence interval [CI], 1.39-3.20) predicted HCV seroconversion. CONCLUSIONS: In the SHCS, HCV infection incidence decreased in IDU, remained stable in HET, and increased 18-fold in MSM in the last 13 years. These observations underscore the need for improved HCV surveillance and prevention among HIV-infected MSM.

Epiphytic lichens as surrogates for biodiversity and ecosystem resilience in native oakwoods of the Baixo Tamega region (Northern Portugal)

In the last 50 years, concern about the loss of lichen diversity associated with forest management and forest fragmentation has led to many studies designed to assess patterns and monitor trends of lichen biodiversity in forests worldwide. However there are surprisingly few studies focusing on the effect of natural disturbance for epiphytic lichens in forest ecosystems and, especially, on how these changes affect the relationships between epiphytic lichens and other organisms. The major goal of this thesis was to characterize and valuate the epiphytic lichens in the Baixo Tamega region (northern Portugal) and to assess its vulnerability to several drivers of change, particularly fire. The study area is located in Aboboreira and Castelo, a mountain area with 105 km2 and a top altitude of approximately 1000 m.a.s.l. In this region, fire is one of the worst natural catastrophes not only because of its high frequency and wide extension but also because of their enormous destructive effects. This thesis has included three case studies that proved the need to develop management and conservation actions for the area. In the first study we assessed the epiphytic lichen diversity in the oak woods of the Aboboreira and Castelo mountains. Results have revealed high diversity value and presence of a lichen community that has suffered general decline throughout Europe. The second study has addressed the impact of fire over epiphytic lichens and community recovering patterns. Results observed along the fire gradient showed that the most common and abundant lichen species establish themselves early in post-fire gradient while “old-growth” associated lichens tend to recover slowly along the same gradient. The third study intended to evaluate the potential use of selected lichen species or groups as biodiversity surrogates, in a scenario of fire-controlled ecological changes. Results showed that the use of epiphytic lichens as surrogates of bryophyte and vascular plant diversity should consider not only species richeness and composition, but also occurrence of disturbing factors, such fire. among the studied groups, lichen genera is the only group that can be used as surrogate of total epiphytic lichen diversity, independently of fire induced changes

Evolution de l'incidence des cancers et des polypes colorectaux dans le canton de Vaud entre 1983 et 2007. [Trends in incidence of colorectal cancers and polyps in the Swiss canton of Vaud 1983-2007].

Colorectal cancer is the second most frequent cancer at death and third most common neoplasm in Switzerland, with about 1600 deaths and 4000 new cases per year, respectively. This study describes the recent trends in colorectal polyps and cancers in the canton of Vaud where a rare population-based series on polyps has been available since 1983. The most salient results are the exponential increase in the detection rates of polyps since the late 19805, associated with a doubling in the proportion of right-sided polyps, whereas colorectal cancer incidence remained constant over the last 25 years. The apparent paradox between the strong increase in detection and resection of polyps, largely due to screening activity, and the absence of reduction in colorectal cancer incidence in the Vaud population is discussed.

Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation.

During the last few years, next-generation sequencing (NGS) technologies have accelerated the detection of genetic variants resulting in the rapid discovery of new disease-associated genes. However, the wealth of variation data made available by NGS alone is not sufficient to understand the mechanisms underlying disease pathogenesis and manifestation. Multidisciplinary approaches combining sequence and clinical data with prior biological knowledge are needed to unravel the role of genetic variants in human health and disease. In this context, it is crucial that these data are linked, organized, and made readily available through reliable online resources. The Swiss-Prot section of the Universal Protein Knowledgebase (UniProtKB/Swiss-Prot) provides the scientific community with a collection of information on protein functions, interactions, biological pathways, as well as human genetic diseases and variants, all manually reviewed by experts. In this article, we present an overview of the information content of UniProtKB/Swiss-Prot to show how this knowledgebase can support researchers in the elucidation of the mechanisms leading from a molecular defect to a disease phenotype.

Theimpact of industry collaboration on research: Evidence from engineering academics in the UK

We study the impact of university-industry research collaborations on academicoutput, in terms of productivity and direction of research. We report findings froma longitudinal dataset on all the researchers from the engineering departments inthe UK in the last 20 years. We control for the endogeneity caused by the dynamicnature of research and the existence of reverse causality. Our results indicate thatresearchers with industrial links publish significantly more. Productivity, though,is higher for low levels of industry involvement. Moreover, growing ties with theindustry skew research towards a more applied approach.

DIGITAL LIBRARIES IN THE DEVELOPING COUNTRIES

Digital libraries (DL) are seen as a hope to developing countries in their struggle for accessing bibliographic resources, especially in a context where the traditional distribution mechanisms failed tragically. Several difficulties are however faced by these countries to build and use digital libraries, due mainly to its high development costs and to the poor existing ICT resources in these countries. This paper discusses the importance of digital libraries for developing countries and introduces the main challenges they face in building and using such libraries. The current alternatives and major initiatives for making digital information accessible to developing countries are also addressed.

The Energy metabolism of China and India between 1971-2010: studying the bifurcation

This paper presents a comparison of the changes in the energetic metabolic pattern of China and India, the two most populated countries in the world, with two economies undergoing an important economic transition. The comparison of the changes in the energetic metabolic pattern has the scope to characterize and explain a bifurcation in their evolutionary path in the recent years, using the Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM) approach. The analysis shows an impressive transformation of China’s energy metabolism determined by the joining of the WTO in 2001. Since then, China became the largest factory of the world with a generalized capitalization of all sectors ―especially the industrial sector― boosting economic labor productivity as well as total energy consumption. India, on the contrary, lags behind when considering these factors. Looking at changes in the household sector (energy metabolism associated with final consumption) in the case of China, the energetic metabolic rate (EMR) soared in the last decade, also thanks to a reduced growth of population, whereas in India it remained stagnant for the last 40 years. This analysis indicates a big challenge for India for the next decade. In the light of the data analyzed both countries will continue to require strong injections of technical capital requiring a continuous increase in their total energy consumption. When considering the size of these economies it is easy to guess that this may induce a dramatic increase in the price of energy, an event that at the moment will penalize much more the chance of a quick economic development of India.

The extended GLUT-family of sugar/polyol transport facilitators: nomenclature, sequence characteristics, and potential function of its novel members (review).

During the last 2 years, several novel genes that encode glucose transporter-like proteins have been identified and characterized. Because of their sequence similarity with GLUT1, these genes appear to belong to the family of solute carriers 2A (SLC2A, protein symbol GLUT). Sequence comparisons of all 13 family members allow the definition of characteristic sugar/polyol transporter signatures: (1) the presence of 12 membrane-spanning helices, (2) seven conserved glycine residues in the helices, (3) several basic and acidic residues at the intracellular surface of the proteins, (4) two conserved tryptophan residues, and (5) two conserved tyrosine residues. On the basis of sequence similarities and characteristic elements, the extended GLUT family can be divided into three subfamilies, namely class I (the previously known glucose transporters GLUT1-4), class II (the previously known fructose transporter GLUT5, the GLUT7, GLUT9 and GLUT11), and class III (GLUT6, 8, 10, 12, and the myo-inositol transporter HMIT1). Functional characteristics have been reported for some of the novel GLUTs. Like GLUT1-4, they exhibit a tissue/cell-specific expression (GLUT6, leukocytes, brain; GLUT8, testis, blastocysts, brain, muscle, adipocytes; GLUT9, liver, kidney; GLUT10, liver, pancreas; GLUT11, heart, skeletal muscle). GLUT6 and GLUT8 appear to be regulated by sub-cellular redistribution, because they are targeted to intra-cellular compartments by dileucine motifs in a dynamin dependent manner. Sugar transport has been reported for GLUT6, 8, and 11; HMIT1 has been shown to be a H+/myo-inositol co-transporter. Thus, the members of the extended GLUT family exhibit a surprisingly diverse substrate specificity, and the definition of sequence elements determining this substrate specificity will require a full functional characterization of all members.

Six Years of Denosumab Treatment in Postmenopausal Women with Osteoporosis: Results From the First Three Years of the FREEDOM Extension

Background/Purpose: Denosumab (DMAb) is an approved therapy for the treatment of postmenopausal women with osteoporosis at increased risk for fracture. A favorable risk/benefit profile was demonstrated in the pivotal, 3-year FREEDOM trial (Cummings et al NEJM 2009). The open-label, active-treatment FREEDOM Extension study is investigating the efficacy and safety of DMAb for up to 10 years. The Extension trial enrolled women who had received DMAb or placebo in FREEDOM and provides an opportunity to evaluate the long-term efficacy and safety of continuous DMAb treatment (long-term group), and to replicate the DMAb findings observed in FREEDOM (cross-over group). Here, we report the results from the first 3 years of the Extension, representing up to 6 continuous years of DMAb exposure. Methods: During the Extension, each woman is scheduled to receive 60 mg DMAb every 6 months and supplemental calcium and vitamin D daily. For the analyses reported here, women from the FREEDOM DMAb group received 3 more years of DMAb for a total of 6 years of exposure (long-term group) and women from the FREEDOM placebo group received 3 years of DMAb exposure (cross-over group). Results: Of the 5928 women eligible for the Extension, 4550 (77%) enrolled (N_2343 long-term; N_2207 cross-over). In the long-term group, further significant mean increases in bone mineral density (BMD) occurred 4044 for cumulative 6-year gains of 15.2% at the lumbar spine and 7.5% at the total hip (Figure). During the first 3 years of DMAb treatment during the Extension, the cross-over group had significant mean gains in BMD at the lumbar spine (9.4%) and total hip (4.8%), similar to those observed in the long-term DMAb group during the first 3 years of FREEDOM (lumbar spine, 10.1%; total hip, 5.7%). Serum CTX was rapidly and similarly reduced after the 1st (cross-over) or 7th (long-term) DMAb dose with the characteristic attenuation observed at the end of the dosing period. In the cross-over group, yearly incidences of new vertebral and nonvertebral fractures were lower than in the FREEDOM placebo group. Fracture incidence remained low in the long-term group. Incidences of adverse events (AEs) and serious AEs did not increase over time with DMAb treatment. There were 2 subjects with AEs adjudicated to ONJ in the cross-over group and 2 in the long-term group. Both cases in the cross-over group healed completely and without further complications; 1 of these subjects continues to receive DMAb. Both women in the long-term group continue to be followed. No atypical femur fractures have been observed to date. Figure. Percent changes in bone mineral density during FREEDOM and the Extension Conclusion: DMAb treatment for 6 continuous years (long-term group) remained well tolerated, maintained reduced bone turnover, and continued to significantly increase BMD. Fracture incidence remained low. DMAb treatment for 3 years in the cross-over group reproduced the original observations in FREEDOM

Transcatheter aortic "valve-in-valve" for degenerated bioprostheses: Choosing the right TAVI valve.

Bioprosthetic aortic valve replacement is the treatment of choice for patients over 65 years of age suffering from aortic valve disease, and for younger patients with contraindications to long-lasting anticoagulation. Despite several technical improvements to reduce the risk of structural valve degeneration (SVD), the risk of SVD still exists, in particular for hemodialysis patients and patients under 60 years of age at surgery. Redo open heart surgery is the treatment of choice in case of valve degeneration, but caries a higher surgical risk when elderly patients with comorbidities are concerned. In the last 5 years, transcatheter aortic "valve-in-valve" procedures represent a valid alternative to standard redo surgery in selected patients. Valve-in-valve procedures represent a less invasive approach in high-risk patients and the published results are very encouraging. Technical success rates of 100% have been reported, as have the absence of paravalvular leaks, acceptable trans-valvular gradients (depending on the size of the original bioprosthesis), and low complication rates. The current article focuses on choosing the correct transcutaneous valve to match the patient's existing bioprosthesis for valve-in-valve procedures.

Decrease in the prevalence of hepatitis B and a low prevalence of hepatitis C virus infections in the general population of the Seychelles.

A serological survey of hepatitis B virus (HBV) and hepatitis C virus (HCV) infections was carried out on a random sex- and age-stratified sample of 1006 individuals aged 25-64 years in the Seychelles islands. Anti-HBc and anti-HCV antibodies were detected using commercially available enzyme-linked immunosorbent assays (ELISA), followed by a Western blot assay in the case of a positive result for anti-HCV. The age-adjusted seroprevalence of anti-HBc antibodies was 8.0% (95% CI: 6.5-9.9%) and the percentage prevalence among males/females increased from 7.0/3.1 to 19.1/13.4 in the age groups 25-34 to 55-64 years, respectively. Two men and three women were positive for anti-HCV antibodies, with an age-adjusted seroprevalence of 0.34% (95% CI: 0.1-0.8%). Two out of these five subjects who were positive for anti-HCV also had anti-HBc antibodies. The seroprevalence of anti-HBc was significantly higher in unskilled workers, persons with low education, and heavy drinkers. The age-specific seroprevalence of anti-HBc in this population-based survey, which was conducted in 1994, was approximately three times lower than in a previous patient-based survey carried out in 1979. Although there are methodological differences between the two surveys, it is likely that the substantial decrease in anti-HBc prevalence during the last 15 years may be due to significant socioeconomic development and the systematic screening of blood donors since 1981. Because hepatitis C virus infections are serious and the cost of treatment is high, the fact that the prevalence of anti-HCV antibodies is at present low should not be an argument for not screening blood donors for anti-HCV and eliminating those who are positive.

Geographic and temporal variation in the consumption of bats by European barn owls

Capsule We report a review of the occurrence of bats in the Barn Owl diet Tyto alba in Europe. Based on 802 studies reporting 4.02 million prey items identified in pellets, 4949 were bats (0.12%). We found that bat predation decreased during the last 150 years, is more frequent on islands than mainland, and is higher in eastern than western Europe and in southern than northern Europe. Although Barn Owls usually capture bats opportunistically, they can sometimes specialize on them.

The Hercynian ore deposits from the Catalonian Coastal Ranges

Many mineralizations, showings and geochemical anomalies have been found in the Hercynian of the Catalonian Coastal Ranges during the last ten years. Many of them are enclosed in the Paleozoic sediments and volcanics and display pre-metamorphic syngenetic characteristics. The lower carboniferous manganese and base meta1 deposits appear to be formed from hydrothermal fluids springing up in the sea floor through active fractures controlling the filling of the basins in a extensional geotectonic setting. Although less evidence and more controversy is available, similar ore forming processes could have taken place in older Paleozoic times. The deformation and metamorphism have not played an important remobilization role, and most epigenetic deposits of Hercynian age are related to the hydrothermal cells induced by the post-metamorphic granitic intrusives.

The UniProt-GO Annotation database in 2011.

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set.