eggNOG v4.0: nested orthology inference across 3686 organisms

With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.

In situ spectroellipsometric study of the nucleation and growth of amorphous silicon

A detailed in situ spectroellipsometric analysis of the nucleation and growth of hydrogenated amorphous silicon (a:Si:H) is presented. Photoelectronic quality a‐Si:H films are deposited by plasma‐enhanced chemical vapor deposition on smooth metal (NiCr alloy) and crystalline silicon (c‐Si) substrates. The deposition of a‐Si:H is analyzed from the first monolayer up to a final thickness of 1.2 μm. In order to perform an improved analysis, real time ellipsometric trajectories are recorded, using fixed preparation conditions, at various photon energies ranging from 2.2 to 3.6 eV. The advantage of using such a spectroscopic experimental procedure is underlined. New insights into the nucleation and growth mechanisms of a‐Si:H are obtained. The nucleation mechanism on metal and c‐Si substrates is very accurately described assuming a columnar microstructural development during the early stage of the growth. Then, as a consequence of the incomplete coalescence of the initial nuclei, a surface roughness at the 10-15 Å scale is identified during the further growth of a‐Si:H on both substrates. The bulk a‐Si:H grows homogeneously beneath the surface roughness. Finally, an increase of the surface roughness is evidenced during the long term growth of a‐Si:H. However, the nature of the substrate influenced the film growth. In particular, the film thickness involved in the nucleation‐coalescence phase is found lower in the case of c‐Si (67±8 Å) as compared to NiCr (118±22 Å). Likewise films deposited on c‐Si present a smaller surface roughness even if thick samples are considered (>1 μm). More generally, the present study illustrates the capability of in situ spectroellipsometry to precisely analyze fundamental processes in thin‐film growth, but also to monitor the preparation of complex structures on a few monolayers scale.

Bivalirudin for patients with acute coronary syndromes

Background: Current guidelines for patients with moderate- or high-risk acute coronary syndromes recommend an early invasive approach with concomitant antithrombotic therapy, including aspirin, clopidogrel, unfractionated or low-molecular-weight heparin, and glycoprotein IIb/IIIa inhibitors. We evaluated the role of thrombin-specific anticoagulation with bivalirudin in such patients. Methods: We assigned 13,819 patients with acute coronary syndromes to one of three antithrombotic regimens: unfractionated heparin or enoxaparin plus a glycoprotein IIb/IIIa inhibitor, bivalirudin plus a glycoprotein IIb/IIIa inhibitor, or bivalirudin alone. The primary end points were a composite ischemia end point (death, myocardial infarction, or unplanned revascularization for ischemia), major bleeding, and the net clinical outcome, defined as the combination of composite ischemia or major bleeding. Results: Bivalirudin plus a glycoprotein IIb/IIIa inhibitor, as compared with heparin plus a glycoprotein IIb/IIIa inhibitor, was associated with noninferior 30-day rates of the composite ischemia end point (7.7% and 7.3%, respectively), major bleeding (5.3% and 5.7%), and the net clinical outcome end point (11.8% and 11.7%). Bivalirudin alone, as compared with heparin plus a glycoprotein IIb/IIIa inhibitor, was associated with a noninferior rate of the composite ischemia end point (7.8% and 7.3%, respectively; P = 0.32; relative risk, 1.08; 95% confidence interval [CI], 0.93 to 1.24) and significantly reduced rates of major bleeding (3.0% vs. 5.7%; P<0.001; relative risk, 0.53; 95% CI, 0.43 to 0.65) and the net clinical outcome end point (10.1% vs. 11.7%; P = 0.02; relative risk, 0.86; 95% CI, 0.77 to 0.97). Conclusions: In patients with moderate- or high-risk acute coronary syndromes who were undergoing invasive treatment with glycoprotein IIb/IIIa inhibitors, bivalirudin was associated with rates of ischemia and bleeding that were similar to those with heparin. Bivalirudin alone was associated with similar rates of ischemia and significantly lower rates of bleeding. (ClinicalTrials.gov number, NCT00093158.)

Thrombin-receptor antagonist vorapaxar in acute coronary syndromes

Background: Vorapaxar is a new oral protease-activated-receptor 1 (PAR-1) antagonist that inhibits thrombin-induced platelet activation. Methods: In this multinational, double-blind, randomized trial, we compared vorapaxar with placebo in 12,944 patients who had acute coronary syndromes without ST-segment elevation. The primary end point was a composite of death from cardiovascular causes, myocardial infarction, stroke, recurrent ischemia with rehospitalization, or urgent coronary revascularization. RESULTS: Follow-up in the trial was terminated early after a safety review. After a median follow-up of 502 days (interquartile range, 349 to 667), the primary end point occurred in 1031 of 6473 patients receiving vorapaxar versus 1102 of 6471 patients receiving placebo (Kaplan-Meier 2-year rate, 18.5% vs. 19.9%; hazard ratio, 0.92; 95% confidence interval [CI], 0.85 to 1.01; P = 0.07). A composite of death from cardiovascular causes, myocardial infarction, or stroke occurred in 822 patients in the vorapaxar group versus 910 in the placebo group (14.7% and 16.4%, respectively; hazard ratio, 0.89; 95% CI, 0.81 to 0.98; P = 0.02). Rates of moderate and severe bleeding were 7.2% in the vorapaxar group and 5.2% in the placebo group (hazard ratio, 1.35; 95% CI, 1.16 to 1.58; P<0.001). Intracranial hemorrhage rates were 1.1% and 0.2%, respectively (hazard ratio, 3.39; 95% CI, 1.78 to 6.45; P<0.001). Rates of nonhemorrhagic adverse events were similar in the two groups. Conclusions: In patients with acute coronary syndromes, the addition of vorapaxar to standard therapy did not significantly reduce the primary composite end point but significantly increased the risk of major bleeding, including intracranial hemorrhage. (Funded by Merck; TRACER ClinicalTrials.gov number, NCT00527943.)

Coarse-graining and thermodynamics in far-from-equilibrium systems

Lying at the core of statistical physics is the need to reduce the number of degrees of freedom in a system. Coarse-graining is a frequently-used procedure to bridge molecular modeling with experiments. In equilibrium systems, this task can be readily performed; however in systems outside equilibrium, a possible lack of equilibration of the eliminated degrees of freedom may lead to incomplete or even misleading descriptions. Here, we present some examples showing how an improper coarse-graining procedure may result in linear approaches to nonlinear processes, miscalculations of activation rates and violations of the fluctuation-dissipation theorem.

Growth and magnetic characterization of Co nanoparticles obtained by femtosecond pulsed laser deposition.

We present a detailed study on the morphology and magnetic properties of Co nanostructures deposited onto oxidized Si substrates by femtosecond pulsed laser deposition. Generally, Co disks of nanometric dimensions are obtained just above the ablation threshold, with a size distribution characterized by an increasingly larger number of disks as their size diminishes, and with a maximum disk size that depends on the laser power density. In Au/Co/Au structures, in-plane magnetic anisotropy is observed in all cases, with no indication of superparamagnetism regardless of the amount of material or the laser power density. Magnetic force microscopy observations show coexistence of single-domain and vortex states for the magnetic domain structure of the disks. Superconducting quantum interference device magnetometry and x-ray magnetic circular dichroism measurements point to saturation magnetization values lower than the bulk, probably due to partial oxidation of the Co resulting from incomplete coverage by the Au capping layer.

Efecto de la temperatura en la tasa de puesta de reinas de la hormiga argentina, Linepithema humile (Mayr, 1868), (Hymenoptera, Dolichoderine) bajo condiciones experimentales de monoginia y poliginia = Effect of temperature on the oviposition rate of the argentine ant queens, Linepithema humile (Mayr 1868), (Hymenoptera, Dolichoderine) under experimental conditions

Data concerning the effect of temperature on different physiological parameters of an invasive species can be a useful tool to predict its potential distribution range through the use of modelling approaches. In the case of the Argentine ant these data are too scarce and incomplete. The aim of the present study is to compile new data regarding the effect of temperature on the oviposition rate of the Argentine ant queens. We analysed the oviposition rate of queens at twelve controlled temperatures, ranging from 10ºC to 34ºC under different monogynous and polygynous conditions. The oviposition rate of the Argentine ant queens is affected by temperature in the same manner, independently of the number of queens in the nest. The optimal temperature for egg laying was 28ºC, and its upper and lower limits depended on the degree of polygyny

Percepción del dolor en pacientes postoperados de cirugía cardiaca

Pain is defined as an unpleasant sensory or emotional experience, associated with tissue damage, that is a reality linked to the surgical procedure and the postoperative period. Objective: Knowing the degree of pain experienced by patients after cardiac surgery, depending on the type of intervention they underwent, over the post-operative period in an intensive care unit (ICU). Method: Descriptive observational study. Pain was assessed by the visual analog scale (VAS), going from 0 to 10, thereby obtaining the first VAS1 assessment at 2 h post-extubation and every 8 hours thereafter up to 48 hours or until discharge to floor VAS7. It included patients having undergone cardiac surgery [valve surgery, bypass, combined procedure (including valve surgery and bypass) and mediastinitis]. Data were processed using Spss.v 20. Results: 120 patients 70 years old on average (standard deviation (SD): 13.3 years old) were included, out of which 70% were male. 40.8% of them had underwent bypass coronary revascularization. Patients subjected to the bypass technique showed an VAS1 mean value of 4.35 (SD: 2.45), unlike those subjected to valve surgery, who showed a mean value of 2.89 (SD: 2.27), those subjected to the combined procedure, who showed a mean value of 3.87 (SD: 2.90), and those with mediastinitis, who showed a mean value of 3.33 (SD: 3.51); (p < 0.031). 28.5% of patients had underwent revascularization (n = 49 ) by an internal mam mary artery (IMA) graft. These patients showed a mean value for VAS1 of 5.4 (SD: 1.89), unlike those who had underwent a combined procedure [IMA and saphenous vein (SV)], who showed a mean value of 3.9 (SD: 2.6), and those who had underwent a SV procedure , who showed a mean value of 3.5 (SD: 2.1); (p < 0.045). Conclusions: Patients having underwent bypass and IMA procedures perceive more pain than in other cardiac surgery and graft interventions

A common cognitive, psychiatric, and dysmorphic phenotype in carriers of NRXN1 deletion

Deletions in the 2p16.3 region that includes the neurexin (NRXN1) gene are associated with intellectual disability and various psychiatric disorders, in particular, autism and schizophrenia. We present three unrelated patients, two adults and one child, in whom we identified an intragenic 2p16.3 deletion within the NRXN1 gene using an oligonucleotide comparative genomic hybridization array. The three patients presented dual diagnosis that consisted of mild intellectual disability and autism and bipolar disorder. Also, they all shared a dysmorphic phenotype characterized by a long face, deep set eyes, and prominent premaxilla. Genetic analysis of family members showed two inherited deletions. A comprehensive neuropsychological examination of the 2p16.3 deletion carriers revealed the same phenotype, characterized by anxiety disorder, borderline intelligence, and dysexecutive syndrome. The cognitive pattern of dysexecutive syndrome with poor working memory and reduced attention switching, mental flexibility, and verbal fluency was the same than those of the adult probands. We suggest that in addition to intellectual disability and psychiatric disease, NRXN1 deletion is a risk factor for a characteristic cognitive and dysmorphic profile. The new cognitive phenotype found in the 2p16.3 deletion carriers suggests that 2p16.3 deletions might have a wide variable expressivity instead of incomplete penetrance

Insulin-Like growth-factor 1 myocardial expression decreases in chronic alcohol consumption

Background Chronic alcohol ingestion may cause severe biochemical and pathophysiological derangements to skeletal muscle. Unfortunately, these alcohol-induced events may also prime skeletal muscle for worsened, delayed, or possibly incomplete repair following acute injury. As alcoholics may be at increased risk for skeletal muscle injury, our goals were to identify the effects of chronic alcohol ingestion on components of skeletal muscle regeneration. To accomplish this, age- and gender-matched C57Bl/6 mice were provided normal drinking water or water that contained 20% alcohol (v/v) for 18-20 wk. Subgroups of mice were injected with a 1.2% barium chloride (BaCl2) solution into the tibialis anterior (TA) muscle to initiate degeneration and regeneration processes. Body weights and voluntary wheel running distances were recorded during the course of recovery. Muscles were harvested at 2, 7 or 14 days post-injection and assessed for markers of inflammation and oxidant stress, fiber cross-sectional areas, levels of growth and fibrotic factors, and fibrosis. Results Body weights of injured, alcohol-fed mice were reduced during the first week of recovery. These mice also ran significantly shorter distances over the two weeks following injury compared to uninjured, alcoholics. Injured TA muscles from alcohol-fed mice had increased TNFα and IL6 gene levels compared to controls 2 days after injury. Total protein oxidant stress and alterations to glutathione homeostasis were also evident at 7 and 14 days after injury. Ciliary neurotrophic factor (CNTF) induction was delayed in injured muscles from alcohol-fed mice which may explain, in part, why fiber cross-sectional area failed to normalize 14 days following injury. Gene levels of TGFβ1 were induced early following injury before normalizing in muscle from alcohol-fed mice compared to controls. However, TGFβ1 protein content was consistently elevated in injured muscle regardless of diet. Fibrosis was increased in injured, muscle from alcohol-fed mice at 7 and 14 days of recovery compared to injured controls. Conclusions Chronic alcohol ingestion appears to delay the normal regenerative response following significant skeletal muscle injury. This is evidenced by reduced cross-sectional areas of regenerated fibers, increased fibrosis, and altered temporal expression of well-described growth and fibrotic factors.

¿Qué entienden los jóvenes universitarios por monogamia y sexo sin penetración, como estrategias preventivas de la transmisión sexual del virus del SIDA? = What university students understand by monogamy and sex without penetration as preventive strategies of sexual transmission of AIDS virus?

Monogamy and sex without penetration are behaviors recommended by the WHO to avoid AIDS virus sexual transmission. Seven hundred and fifty university students from 18 to 25 years (67.7% women) were surveyed and they were asked to give a maximum of three free definitions of the words monogamy and sex without penetration to prevent AIDS virus sexual transmission. Their participation was voluntary and anonymous. Although the majority of the answers was correct, there was a considerable percentage of wrong answers, either for monogamy (3.7% masturbation; 2.1% to have many partners; 0.9% homosexual relations), or for sex without penetration (20.5% oral sex; 1.1% anal coitus; 0.8% coitus without orgasm; 0.4% coitus interruptus). Some definitions or examples differ by gender. The amount of wrongs or incomplete answers put researchers on the alert about insufficient preventive knowledge in a population with a high educational level