Phthalates in the NICU: Is it safe?

AIMS: As growing concerns exist regarding phthalate exposure, which could be teratogenic, carcinogenic or induce reproductive toxicity, we aimed to review the evidence of the risks due to the use of medical devices containing di(2-ethylhexyl)phthalate in hospitalized neonates. METHODS: We reviewed the literature, searching through medical literature databases (Pubmed, MEDLINE, EBM reviews, Cochrane database, Embase and Google Scholar) using the following keywords: phthalate, di(2-ethylhexyl)phthalate, newborn and neonate. RESULTS: We identified several associations with short and long term health dangers, mainly subfertility, broncho-pulmonary dysplasia, necrotising enterocolitis, parenteral nutrition associated cholestasis and neuro-developmental disorders. These data are based mainly on animal or observational human studies. CONCLUSION: Clinicians must be aware of the potential risks due to phthalate exposure in the NICU. Di(2-ethylhexyl)phthalate containing materials should be identified and alternative devices should be considered. There is a need to improve knowledge in this area.

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.

Database construction and Peptide identification strategies for proteogenomic studies on sequenced genomes.

Since the advent of high-throughput DNA sequencing technologies, the ever-increasing rate at which genomes have been published has generated new challenges notably at the level of genome annotation. Even if gene predictors and annotation softwares are more and more efficient, the ultimate validation is still in the observation of predicted gene product( s). Mass-spectrometry based proteomics provides the necessary high throughput technology to show evidences of protein presence and, from the identified sequences, confirmation or invalidation of predicted annotations. We review here different strategies used to perform a MS-based proteogenomics experiment with a bottom-up approach. We start from the strengths and weaknesses of the different database construction strategies, based on different genomic information (whole genome, ORF, cDNA, EST or RNA-Seq data), which are then used for matching mass spectra to peptides and proteins. We also review the important points to be considered for a correct statistical assessment of the peptide identifications. Finally, we provide references for tools used to map and visualize the peptide identifications back to the original genomic information.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis x Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Appraising and selecting strategies to combat and mitigate desertification based on stakeholder knowledge and globalbest practices in Cape Verde Archipelago

Cape Verde is considered part of Sahelian Africa, where drought and desertification are common occurrences. The main activity of the rural population is rain-fed agriculture, which over time has been increasingly challenged by high temporal and spatial rainfall variability, lack of inputs, limited land area, fragmentation of land, steep slopes, pests, lack of mechanization and loss of top soil by water erosion. Human activities, largely through poor farming practices and deforestation (Gomez, 1989) have accelerated natural erosion processes, shifting the balance between soil erosion and soil formation (Norton, 1987). According to previous studies, vegetation cover is one of the most important factors in controlling soil loss (Cyr et al., 1995; Hupy, 2004; Zhang et al., 2004; Zhou et al., 2006). For this reason, reforestation is a touchstone of the Cape Verdean policy to combat desertification. After Independence in 1975, the Cape Verde government had pressing and closely entangled environmental and socio-economic issues to address, as long-term desertification had resulted in a lack of soil cover, severe soil erosion and a scarcity of water resources and fuel wood. Across the archipelago, desertification was resulting from a variety of processes including poor farming practices, soil erosion by water and wind, soil and water salinity in coastal areas due to over pumping and seawater intrusion, drought and unplanned urbanization (DGA-MAAP, 2004). All these issues directly affected socio-economic vulnerability in rural areas, where about 70% of people depended directly or indirectly on agriculture in 1975. By becoming part of the Inter- State Committee for the Fight against Drought in the Sahel in 1975, the government of Cape Verde gained structured support to address these issues more efficiently. Presentday policies and strategies were defined on the basis of rational use of resources and human efforts and were incorporated into three subsequent national plans: the National Action Plan for Development (NDP) (1982–1986), the NDP (1986–1990) and the NDP (1991–1995) (Carvalho

ViralZone: a knowledge resource to understand virus diversity.

The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators must be familiar with the virus host range, replication cycle and virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.

Record keeping by Swiss physiotherapists--a national survey of knowledge regarding legal requirements.

A national survey conducted in Switzerland aimed to evaluate the knowledge of physiotherapists regarding the legal requirements for record keeping and to collect their feedback about record keeping in general. Three physiotherapists from various professional practice groups and a lawyer specialised in health law developed a questionnaire that was sent to the 7,753 members of two existing national associations of physiotherapists. The questionnaire evaluated the participants' knowledge by calculating a score of legal knowledge, which had a maximum of 30 points. We included 825 questionnaires in the analysis. The large majority (83.4%) of participants confessed an ignorance of the legal requirements concerning record keeping prior to the survey. The average score of legal compatibility was 8 points. The younger age of the physiotherapists was a significant predictor of having knowledge of the legal requirements for record keeping (p <0.001). The participants had an appreciation of the value of records, but they did not have the relevant knowledge regarding the legal requirements for keeping records. The participants blamed a lack of time and remuneration for their failure to keep records according to known requirements. All practising allied health professionals should keep up-to-date and accurate records that conform to active legal requirements and existing international guidelines. In addition to the existing legal requirements, the emergence of e-health and the electronic era will trigger major changes in patient record management by physiotherapists.

Contributions to the knowledge of Banasa Stål (Hemiptera, Heteroptera, Pentatomidae): Banasa chaca Thomas

Contributions to the knowledge of Banasa Stål (Hemiptera, Heteroptera, Pentatomidae): Banasa chaca Thomas. The male of Banasa chaca Thomas is described with emphasis on external and internal genitalia and the female internal genitalia is described. Banasa chaca is newly recorded from Buenos Aires Province (Argentina).

On heuristic and linear models of judgment: Mapping the demand for knowledge

Research on judgment and decision making presents a confusing picture of human abilities. For example, much research has emphasized the dysfunctional aspects of judgmental heuristics, and yet, other findings suggest that these can be highly effective. A further line of research has modeled judgment as resulting from as if linear models. This paper illuminates the distinctions in these approaches by providing a common analytical framework based on the central theoretical premise that understanding human performance requires specifying how characteristics of the decision rules people use interact with the demands of the tasks they face. Our work synthesizes the analytical tools of lens model research with novel methodology developed to specify the effectiveness of heuristics in different environments and allows direct comparisons between the different approaches. We illustrate with both theoretical analyses and simulations. We further link our results to the empirical literature by a meta-analysis of lens model studies and estimate both human andheuristic performance in the same tasks. Our results highlight the trade-off betweenlinear models and heuristics. Whereas the former are cognitively demanding, the latterare simple to use. However, they require knowledge and thus maps of when andwhich heuristic to employ.

Study of the mayfly order Ephemeroptera (Insecta) in Brazil: a scienciometric review

Study of the mayfly order Ephemeroptera (Insecta) in Brazil: a scienciometric review. Despite an increase in the number of studies in recent years of the aquatic insect order Ephemeroptera (the mayflies) much still remains to be learnt. In order to identify the current state of knowledge of this group in Brazil, we performed a scienciometric analysis with the purpose of identifying the strong and weak points of Brazilian research into the group. Our research used the "Institute for Scientific Information - ISI" database and was based on the abstracts, titles and keywords of manuscripts published between 1992 and 2011. We selected the papers with the combination of the words "Ephemeroptera" and "Brazil*" based on a search in February 2012. We analyzed 92 articles, and noted a lack of studies in some Brazilian states, no specific studies about some families, and an absence of phylogenetic studies. To improve ecological studies, it is necessary to fine-tune taxonomic resolution. Moreover, there is a lack of studies investigating the environmental variables which influence the distribution of mayflies. Despite these gaps, if the rate of publication with mayflies proceeds at the same pace, we anticipate that many of these knowledge gaps will be closed.

Superficial soft tissue sarcomas (S-STS): a study of 367 patients from the French Sarcoma Group (FSG) database.

AIM: The specific natural history of superficial soft tissue sarcomas (S-STS) has been rarely considered. We describe the clinical characteristics of a large series of S-STS (N=367) from the French Sarcoma Group (GSF-GETO) database and analyse the prognostic factors affecting outcome. METHODS: We performed univariate and multivariate analyses for overall survival (OS), metastasis-free survival (MFS) and local recurrence-free survival (LRFS). RESULTS: The median age was 59 years. Fifty-eight percent patients were female. Tumour locations were as follows: extremities, 55%; trunk wall, 35.4%; head and neck, 8% and unknown, 1.6%. Median tumour size was 3.0 cm. The most frequent tumour types were unclassified sarcoma (24.3%) and leiomyosarcoma (22.3%). Thirty-three percent of cases were grade 3. Median follow-up was 6.18 years. The 5-year OS, MFS and LRFS rates were 80.9%, 80.7% and 74.7%, respectively. Multivariate analysis retained histological type and wide resection for predicting LRFS and histological type and grade as prognostic factors of MFS. The factors influencing OS were age, histological type, grade and wide resection. STS with early invasion into but not through the underlying fascia had a significantly poorer MFS than with strict S-STS. CONCLUSION: S-STS represent a separate category characterised by a better outcome. Adequate surgery, i.e. wide resection, is essential in the management of S-STS.

An estimate of the potential number of mayfly species (Ephemeroptera, Insecta) still to be described in Brazil

ABSTRACTThis study reviewed the data on the Brazilian Ephemeroptera, based on the studies published before July, 2013, estimated the number of species still to be described, and identified which regions of the country have been the subject of least research. More than half the species are known from the description of only one developmental stage, with imagoes being described more frequently than nymphs. The Brazilian Northeast is the region with the weakest database. Body size affected description rates, with a strong tendency for the larger species to be described first. The estimated number of unknown Brazilian species was accentuated by the fact that so few species have been described so far. The steep slope of the asymptote and the considerable confidence interval of the estimate reinforce the conclusion that a large number of species are still to be described. This emphasizes the need for investments in the training of specialists in systematics and ecology for all regions of Brazil to correct these deficiencies, given the role of published papers as a primary source of information, and the fundamental importance of taxonomic knowledge for the development of effective measures for the conservation of ephemeropteran and the aquatic ecosystems they depend on.

Feasibility of a knowledge translation CME program: courriels Cochrane.

INTRODUCTION: Systematic literature reviews provide best evidence, but are underused by clinicians. Thus, integrating Cochrane reviews into continuing medical education (CME) is challenging. We designed a pilot CME program where summaries of Cochrane reviews (Courriels Cochrane) were disseminated by e-mail. Program participants automatically received CME credit for each Courriel Cochrane they rated. The feasibility of this program is reported (delivery, participation, and participant evaluation). METHOD: We recruited French-speaking physicians through the Canadian Medical Association. Program delivery and participation were documented. Participants rated the informational value of Courriels Cochrane using the Information Assessment Method (IAM), which documented their reflective learning (relevance, cognitive impact, use for a patient, expected health benefits). IAM responses were aggregated and analyzed. RESULTS: The program was delivered as planned. Thirty Courriels Cochrane were delivered to 985 physicians, and 127 (12.9%) completed at least one IAM questionnaire. Out of 1109 Courriels Cochrane ratings, 973 (87.7%) conta-ined 1 or more types of positive cognitive impact, while 835 (75.3%) were clinically relevant. Participants reported the use of information for a patient and expected health benefits in 595 (53.7%) and 569 (51.3%) ratings, respectively. DISCUSSION: Program delivery required partnering with 5 organizations. Participants valued Courriels Cochrane. IAM ratings documented their reflective learning. The aggregation of IAM ratings documented 3 levels of CME outcomes: participation, learning, and performance. This evaluation study demonstrates the feasibility of the Courriels Cochrane as an approach to further disseminate Cochrane systematic literature reviews to clinicians and document self-reported knowledge translation associated with Cochrane reviews.

Global Genomic Diversity of Human Papillomavirus 6 Based on 724 Isolates and 190 Complete Genome Sequences.

Human papillomavirus type 6 (HPV6) is the major etiological agent of anogenital warts and laryngeal papillomas and has been included in both the quadrivalent and nonavalent prophylactic HPV vaccines. This study investigated the global genomic diversity of HPV6, using 724 isolates and 190 complete genomes from six continents, and the association of HPV6 genomic variants with geographical location, anatomical site of infection/disease, and gender. Initially, a 2,800-bp E5a-E5b-L1-LCR fragment was sequenced from 492/530 (92.8%) HPV6-positive samples collected for this study. Among them, 130 exhibited at least one single nucleotide polymorphism (SNP), indel, or amino acid change in the E5a-E5b-L1-LCR fragment and were sequenced in full. A global alignment and maximum likelihood tree of 190 complete HPV6 genomes (130 fully sequenced in this study and 60 obtained from sequence repositories) revealed two variant lineages, A and B, and five B sublineages: B1, B2, B3, B4, and B5. HPV6 (sub)lineage-specific SNPs and a 960-bp representative region for whole-genome-based phylogenetic clustering within the L2 open reading frame were identified. Multivariate logistic regression analysis revealed that lineage B predominated globally. Sublineage B3 was more common in Africa and North and South America, and lineage A was more common in Asia. Sublineages B1 and B3 were associated with anogenital infections, indicating a potential lesion-specific predilection of some HPV6 sublineages. Females had higher odds for infection with sublineage B3 than males. In conclusion, a global HPV6 phylogenetic analysis revealed the existence of two variant lineages and five sublineages, showing some degree of ethnogeographic, gender, and/or disease predilection in their distribution. IMPORTANCE: This study established the largest database of globally circulating HPV6 genomic variants and contributed a total of 130 new, complete HPV6 genome sequences to available sequence repositories. Two HPV6 variant lineages and five sublineages were identified and showed some degree of association with geographical location, anatomical site of infection/disease, and/or gender. We additionally identified several HPV6 lineage- and sublineage-specific SNPs to facilitate the identification of HPV6 variants and determined a representative region within the L2 gene that is suitable for HPV6 whole-genome-based phylogenetic analysis. This study complements and significantly expands the current knowledge of HPV6 genetic diversity and forms a comprehensive basis for future epidemiological, evolutionary, functional, pathogenicity, vaccination, and molecular assay development studies.