efam: an expanded, metaproteome-supported HMM profile database of viral protein families

Motivation: Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Results: Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, panecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from 'conservative' to 'eXtremely Conservative' resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by similar to 24% on average (up to similar to 42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem

Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome

Cognitive appraisal of environmental stimuli induces emotion-like states in fish

The occurrence of emotions in non-human animals has been the focus of debate over the years. Recently, an interest in expanding this debate to non-tetrapod vertebrates and to invertebrates has emerged. Within vertebrates, the study of emotion in teleosts is particularly interesting since they represent a divergent evolutionary radiation from that of tetrapods, and thus they provide an insight into the evolution of the biological mechanisms of emotion. We report that Sea Bream exposed to stimuli that vary according to valence (positive, negative) and salience (predictable, unpredictable) exhibit different behavioural, physiological and neuromolecular states. Since according to the dimensional theory of emotion valence and salience define a two-dimensional affective space, our data can be interpreted as evidence for the occurrence of distinctive affective states in fish corresponding to each the four quadrants of the core affective space. Moreover, the fact that the same stimuli presented in a predictable vs. unpredictable way elicited different behavioural, physiological and neuromolecular states, suggests that stimulus appraisal by the individual, rather than an intrinsic characteristic of the stimulus, has triggered the observed responses. Therefore, our data supports the occurrence of emotion-like states in fish that are regulated by the individual's perception of environmental stimuli.European Commission [265957 Copewell]; Fundacao para a Ciencia e Tecnologia [SFRH/BD/80029/2011, SFRH/BPD/72952/2010]info:eu-repo/semantics/publishedVersio

Immobilization, Trapping, and Anion Exchange of Perrhenate Ion Using Copper-Based Tripodal Complexes

We describe a multidentate tripodal ligand in which three pendant arms carrying di(2-picolyl)amine units are linked to the ortho positions of a tris(o-xylyl) scaffold, providing N(CH[subscript 2]-o-C[subscript 6]H[subscript 4]CH[subscript 2]N(CH2py)[subscript 2])[subscript 3] (L). Reaction of L with CuCl[subscript 2] in the presence of hexafluorophosphate anion afforded blue cubes of [(CuCl)[subscript 3]L](PF[subscript 6])[subscript 3]·5H[subscript 2]O (1). Crystallographic studies of 1 revealed that the three symmetry-related arms each coordinate a {Cu[superscript II]Cl} unit, and two molecules of 1 are connected to one another through a Cu(μ-Cl)[subscript 2]Cu bridge, extending the molecular structure to form a two-dimensional (2-D) layer. These 2-D layers pack in an ABCABC... fashion with PF[subscript 6]– anions located in between. Reaction of 1 with a stoichiometric amount of perrhenate ion afforded blue plates of [(CuCl)[subscript 3]L](PF[subscript 6])(ReO[subscript 4])[subscript 2]·3H[subscript 2]O (2). Compound 2 has the same lattice structure as 1, but the tricopper unit backbone now traps one ReO[subscript 4]– anion through Coulombic interactions. In addition, three molecules of 2 are bridged by a perrhenate ion, forming a Cu[subscript 3](μ[superscript 3]-ReO[subscript 4]) cluster, to give a different 2-D structure displaying a rare tridentate bridging ReO[subscript 4]– mode. Thus, in addition to classic perrhenate trapping through weak Coulombic interactions, 2 represents an exceptional example in which the ReO[subscript 4]– anion is immobilized in an extended framework through tight covalent interactions. The interlamellar PF[subscript 6]– anions in 1 can be exchanged with other anions including perrhenate, perchlorate, or periodate. The structural similarity between perrhenate and pertechnetate makes these materials of potential interest for pertechnetate trapping

Gene expression changes and community turnover differentially shape the global ocean metatranscriptome

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms

An international collaborative evaluation of central serous chorioretinopathy: different therapeutic approaches and review of literature. The European Vitreoretinal Society central serous chorioretinopathy study

Purpose: To study and compare the efficacy of different therapeutic options for the treatment of central serous chorioretinopathy (CSCR). Methods: This is a nonrandomized, international multicentre study on 1719 patients (1861 eyes) diagnosed with CSCR, from 63 centres (24 countries). Reported data included different methods of treatment and both results of diagnostic examinations [fluorescein angiography and/or optical coherent tomography (OCT)] and best-corrected visual acuity (BCVA) before and after therapy. The duration of observation had a mean of 11&nbsp;months but was extended in a minority of cases up to 7&nbsp;years. The aim of this study is to evaluate the efficacy of the different therapeutic options of CSCR in terms of both visual (BCVA) and anatomic (OCT) improvement. Results: One thousand seven hundred nineteen patients (1861 eyes) diagnosed with CSCR were included. Treatments performed were nonsteroidal anti-inflammatory eye drops, laser photocoagulation, micropulse diode laser photocoagulation, photodynamic therapy (PDT; Standard PDT, Reduced-dose PDT, Reduced-fluence PDT), intravitreal (IVT) antivascular endothelial growth factor injection (VEGF), observation and other treatments. The list of the OTHERS included both combinations of the main proposed treatments or a variety of other treatments such as eplerenone, spironolactone, acetazolamide, beta-blockers, anti-anxiety drugs, aspirin, folic acid, methotrexate, statins, vitis vinifera extract medication and pars plana vitrectomy. The majority of the patients were men with a prevalence of 77%. The odds ratio (OR) showed a partial or complete resolution of fluid on OCT with any treatment as compared with observation. In univariate analysis, the anatomical result (improvement in subretinal fluid using OCT at 1&nbsp;month) was favoured by age &lt;60&nbsp;years (p&nbsp;&lt;&nbsp;0.005), no previous observation (p&nbsp;&lt;&nbsp;0.0002), duration less than 3&nbsp;months (p&nbsp;&lt;&nbsp;0.0001), absence of CSCR in the fellow eye (p&nbsp;=&nbsp;0.04), leakage outside of the arcade (p&nbsp;=&nbsp;0.05) and fluid height &gt;500&nbsp;\u3bcm (p&nbsp;=&nbsp;0.03). The OR for obtaining partial or complete resolution showed that anti-VEGF and eyedrops were not statistically significant; whereas PDT (8.5), thermal laser (11.3) and micropulse laser (8.9) lead to better anatomical results with less variability. In univariate analysis, the functional result at 1&nbsp;month was favoured by first episode (p&nbsp;=&nbsp;0.04), height of subretinal fluid &gt;500&nbsp;\u3bcm (p&nbsp;&lt;&nbsp;0.0001) and short duration of observation (p&nbsp;=&nbsp;0.02). Finally, there was no statistically significant difference among the treatments at 12&nbsp;months. Conclusion: Spontaneous resolution has been described in a high percentage of patients. Laser (micropulse and thermal) and PDT seem to lead to significant early anatomical improvement; however, there is little change beyond the first month of treatment. The real visual benefit needs further clarification

Factors associated with hospital service satisfaction in a sample of Arab subjects with schizophrenia

<p>Abstract</p> <p>Background</p> <p>Assessment of patients' satisfaction with health care services could help to identify the strengths and weaknesses of the system and provide guidance for further development. The study's objectives were to: (i) assess the pattern of satisfaction with hospital care for a sample of people with schizophrenia in Kuwait, using the Verona Service Satisfaction Scale (VSSS-EU); ii) compare the pattern of satisfaction with those of similar studies; and iii) assess the association of VSSS seven domains with a number of variables representing met and unmet needs for care, family caregiver burden, severity of psychopathology, level of psychosocial functioning, socio-demographic characteristics, psychological well-being and objective quality of life.</p> <p>Methods</p> <p>Consecutive outpatients in stable condition and their family caregivers were interviewed with the VSSS-EU and measures of needs for care, caregiver burden, quality of life and psychopathology.</p> <p>Results</p> <p>There were 130 patients (66.1%m, mean age 36.8). While over two-thirds expressed satisfaction with the domains of "overall satisfaction", "professionals' skills", "access", "efficacy", and "relatives' involvement", only about one-third were satisfied with the domains of "information" and "types of intervention". The later two domains were the areas in which European patients had better satisfaction than our patients, while our patients expressed better satisfaction than the Europeans in the domain of "relatives' involvement". In multiple regression analyses, self-esteem, positive and negative affect were the most important correlates of the domains of service satisfaction, while clinical severity, caregiver burden and health unmet needs for care played relatively minor roles.</p> <p>Conclusion</p> <p>The noted differences and similarities with the international data, as well as the predictive power of self-esteem and affective state, support the impression that patients' attitudes towards psychiatric care involve a complex relationship between clinical, personal and socio-cultural characteristics; and that many of the factors that impact on satisfaction with service relate to individual psychological characteristics. The weaknesses in the system, highlighted by the pattern of responses of the participants, indicate possible gaps in the provision of comprehensive psychiatric care in the country and obviate the need for public mental health education and development of services to enhance the quality of care.</p

Medication errors in the Middle East countries: a systematic review of the literature

Background: Medication errors are a significant global concern and can cause serious medical consequences for patients. Little is known about medication errors in Middle Eastern countries. The objectives of this systematic review were to review studies of the incidence and types of medication errors in Middle Eastern countries and to identify the main contributory factors involved. Methods: A systematic review of the literature related to medication errors in Middle Eastern countries was conducted in October 2011 using the following databases: Embase, Medline, Pubmed, the British Nursing Index and the Cumulative Index to Nursing & Allied Health Literature. The search strategy included all ages and languages. Inclusion criteria were that the studies assessed or discussed the incidence of medication errors and contributory factors to medication errors during the medication treatment process in adults or in children. Results: Forty-five studies from 10 of the 15 Middle Eastern countries met the inclusion criteria. Nine (20%) studies focused on medication errors in paediatric patients. Twenty-one focused on prescribing errors, 11 measured administration errors, 12 were interventional studies and one assessed transcribing errors. Dispensing and documentation errors were inadequately evaluated. Error rates varied from 7.1% to 90.5% for prescribing and from 9.4% to 80% for administration. The most common types of prescribing errors reported were incorrect dose (with an incidence rate from 0.15% to 34.8% of prescriptions), wrong frequency and wrong strength. Computerised physician rder entry and clinical pharmacist input were the main interventions evaluated. Poor knowledge of medicines was identified as a contributory factor for errors by both doctors (prescribers) and nurses (when administering drugs). Most studies did not assess the clinical severity of the medication errors. Conclusion: Studies related to medication errors in the Middle Eastern countries were relatively few in number and of poor quality. Educational programmes on drug therapy for doctors and nurses are urgently needed