Genetic information improves the prediction of major adverse cardiovascular events in the GENEMACOR population

The inclusion of a genetic risk score (GRS) can modify the risk prediction of coronary artery disease (CAD), providing an advantage over the use of traditional models. The predictive value of the genetic information on the recurrence of major adverse cardiovascular events (MACE) remains controversial. A total of 33 genetic variants previously associated with CAD were genotyped in 1587 CAD patients from the GENEMACOR study. Of these, 18 variants presented an hazard ratio >1, so they were selected to construct a weighted GRS (wGRS). MACE discrimination and reclassification were evaluated by C-Statistic, Net Reclassification Index and Integrated Discrimination Improvement methodologies. After the addition of wGRS to traditional predictors, the C-index increased from 0.566 to 0.572 (p=0.0003). Subsequently, adding wGRS to traditional plus clinical risk factors, this model slightly improved from 0.620 to 0.622 but with statistical significance (p=0.004). NRI showed that 17.9% of the cohort was better reclassified when the primary model was associated with wGRS. The Kaplan-Meier estimator showed that, at 15-year follow-up, the group with a higher number of risk alleles had a significantly higher MACE occurrence (p=0.011). In CAD patients, wGRS improved MACE risk prediction, discrimination and reclassification over the conventional factors, providing better cost-effective therapeutic strategies.     

Taxonomic changes in palaeotropical Xyleborini (Coleoptera, Curculionidae, Scolytinae)

Following the recent reclassification of the Palaeotropic xyleborine genera (Hulcr and Cognato in press), additional species are transferred to correct genera or synonymized based on analysis of their morphological characters. The following species are given new combinations: Debus amphicranoides (Hagedorn), comb. n., Debus birmanus (Eggers, 1930), comb. n., Debus dolosus (Blandford, 1896), comb. n., Debus eximius (Schedl, 1970), comb. n., Debus interponens (Schedl, 1954), comb. n., Debus robustipennis (Schedl, 1954), comb. n., Debus spinatus (Eggers, 1923), comb. n., Microperus alpha (Beeson, 1929), comb. n., Microperus corporaali (Eggers), comb. n., Microperus eucalyptica (Schedl, 1938), comb. n., Microperus nugax (Schedl, 1939), comb. n., Pseudowebbia percorthylus (Schedl, 1935), comb. n., Truncaudum circumcinctus (Schedl, 1941), comb. n.THE FOLLOWING SPECIES ARE SYNONYMIZED: Arixyleborus hirtipennis (Eggers), syn. n., with Arixyleborus puberulus (Blandford); Coptoborus palmeri (Hopkins), syn. n., with Debus emarginatus (Eichhoff); Coptoborus terminaliae (Hopkins), syn. n., with Debus emarginatus (Eichhoff); Cyclorhipidion polyodon (Eggers), syn. n., with Truncaudum agnatum (Eggers); Euwallacea artelaevis (Schedl), syn. n., with Planiculus bicolor (Blandford); Xyleborinus perminutissimus (Schedl), syn. n., with Xyleborinus perpusillus (Eggers); Xyleborus exesus Blandford, syn. n., with Debus emarginatus (Eichhoff); Xyleborus fulvulus (Schedl), syn. n., with Microperus corporaali (Eggers); Xyleborus marginicollis (Schedl), syn. n., with Diuncus justus (Schedl); Xyleborus shoreae Stebbing, syn. n., with Debus fallax (Eichhoff).THE FOLLOWING SPECIES ARE GIVEN NEW STATUS: Streptocranus superbus (Schedl, 1951), restored name; Webbia divisus Browne, 1972, restored name; Webbia penicillatus (Hagedorn, 1910), restored name. Genus Taphrodasus Wood (1980) is declared not valid.     

Evolutionary relationships between mono- and polystiliferous hoplonemerteans: Nipponnemertes (Cratenemertidae), a “missing link” genus?

Histological studies on several species of the monostiliferous hoplonemertean genus Nipponnemertes show that they share certain significant features with reptantic Polystilifera. A brief survey of these features provides a basis for an analysis of possible evolutionary relationships between mono- and polystiliferous Hoplonemertea. It is suggested that ancestral enoplans possessed a rhynchocoel wall containing two muscle layers and a simple protopolystiliferous type of proboscis armature, and that this ancestral pool gave rise to two distinct evolutionary lineages, one leading to cratenemertid, group 2 terrestrial and freshwater, and polystiliferous hoplonemerteans, the other to the typical modern monostiliferous forms. A reclassification of the Enopla is proposed.     

化石直脉蝎蛉科再分类(长翅目)

本文对化石直脉蝎蛉科(Orthophlebiidae)的分属做了再分类,仍保留该科内的 2个属:直脉蝎蛉属 Orthophlebia和原直脉蝎蛉属Protorthophlebia,解体中蝎蛉属Mesopanorpa。中蝎蛉属被解体后,其包含所有的种,如Rs1主干带3支或3支以上支脉,归入直脉蝎蛉属;如Rs1仅带2支支脉,归入原直脉蝎蛉属;原中蝎蛉属以Rs主干两倍长于MA主干作为属的分类根据,但这一属征常常导致分类上的混乱,故本文不作为属或亚属的分类根据。上述保留的2个属,再以Rs分支先于、后于或等于MA的特征,即Rs主干短于、长于或等于MA主干作为亚属的分类根据。以此,在直脉蝎蛉属Orthophlebia和原直脉蝎蛉属Protorthophlebia之下各自设立3个亚属(Hong et Zhang, 2004)。在已建立的6个亚属中,Orthophlebia(Brachyphlebia)Hong et Zhang, 2004和Protorthophlebia(Mecynophlebia)Hong et Zhang,2004分别修改为Orthophlebia(Orthophlebia)Westwood, 1845和Protorthophlebia(Protorthophlebia)Tillyard,1933的新异名。中生代直脉蝎蛉中脉的前支(MA)并非在古生代之后就完全消失。根据对中生代不同时期、不同层位、不同地区直脉蝎蛉和本目其他科在内化石标本的观察,中脉及其前、后支脉(MA、MP)仍然继续存在与发展。基于这种事实,本文认为直脉蝎蛉科脉序命名中沿用已久的Rs后支(Rs3 4)应为中脉的前支(MA),原来沿用的中脉(M)为中脉的后支(MP)。这样,有助于我们对长翅目中脉及其前、后(MA、MP)支脉的准确辨认,尤其是对MA脉在地史上变革、发展,以及与Rs脉的演化关系的认识可能有所裨益。     

Recent developments in QM/MM methods towards open-boundary multi-scale simulations

Combined quantum mechanics/molecular mechanics (QM/MM) methods have been widely used in multi-scale modelling and simulations of physical, chemical and biological processes in complex environments. In this review, we provide an overview of the recently developed QM/MM algorithms, with emphasis on our works, towards the ultimate goal of establishing an open boundary between the QM and MM subsystems. The open boundary is characterised by on-the-fly exchanges of partial charges and atoms between the QM and MM subsystems, allowing us to focus on the small QM subsystem of primary interest in dynamics simulations. An open-boundary scheme has the promise to the utilisations of small QM subsystems, high-levels of QM theory and long simulation times, which can potentially lead to new insights.     

Inference for reclassification statistics under nested and non-nested models for biomarker evaluation

Abstract

The Net Reclassification Improvement (NRI) and the Integrated Discrimination Improvement (IDI) are used to evaluate the diagnostic accuracy improvement for biomarkers in a wide range of applications. Most applications for these reclassification metrics are confined to nested model comparison. We emphasize the important extensions of these metrics to the non-nested comparison. Non-nested models are important in practice, in particular, in high-dimensional data analysis and in sophisticated semiparametric modeling. We demonstrate that the assessment of accuracy improvement may follow the familiar NRI and IDI evaluation. While the statistical properties of the estimators for NRI and IDI have been well studied in the nested setting, one cannot always rely on these asymptotic results to implement the inference procedure for practical data, especially for testing the null hypothesis of no improvement, and these properties have not been established for the non-nested setting. We propose a generic bootstrap re-sampling procedure for the construction of confidence intervals and hypothesis tests. Extensive simulations and real biomedical data examples illustrate the applicability of the proposed inference methods for both nested and non-nested models.     

Land‐use changes as major drivers of mountain pine (Pinus uncinata Ram.) expansion in the Pyrenees

Aim To assess the spatial patterns of forest expansion (encroachment and densification) for mountain pine (Pinus uncinata Ram.) during the last 50 years at a whole mountain range scale by the study of different topographic and socio‐economic potential drivers in the current context of global change. Location The study area includes the whole distributional area of mountain pine in the Catalan Pyrenees (north‐east Spain). This represents more than 80 municipalities, covering a total area of 6018 km². Methods Forest cover was obtained by image reclassification of more than 200 pairs of aerial photographs taken in 1956 and 2006. Encroachment and densification were determined according to changes in forest cover, and were expressed as binary variables on a 150 × 150 m cell‐size grid. We then used logistic regression to analyse the effects of several topographic and socio‐economic variables on forest expansion. Results In the period analysed, mountain pine increased its surface coverage by 8898 ha (an increase of more than 16%). Mean canopy cover rose from 31.0% in 1956 to 55.6% in 2006. Most of the expansion was found on north‐facing slopes and at low altitudes. Socio‐economic factors arose as major factors in mountain pine expansion, as encroachment rates were higher in municipalities with greater population losses or weaker primary sector development. Main conclusions The spatial patterns of mountain pine expansion showed a good match with the main patterns of land‐use change in the Pyrenees, suggesting that land‐use changes have played a more important role than climate in driving forest dynamics at a landscape scale over the period studied. Further studies on forest expansion at a regional scale should incorporate patterns of land‐use changes to correctly interpret drivers of forest encroachment and densification.     

Proposal to transfer Flavobacterium oceanosedimentum Carty and Litchfield 1978 to the genus Curtobacterium as Curtobacterium oceanosedimentum comb. nov.

Flavobacterium oceanosedimentum Carty & Litchfield 1978^AL had been described as a novel species in the genus Flavobacterium on the basis of phenotypic characteristics, although the organism shows a high G+C content, a property never found in the other members of the genus. In this study, we re-evaluated the taxonomic position of F. oceanosedimentum using a polyphasic approach. The 16S rRNA gene sequence of F. oceanosedimentum ATCC 31717^T indicated that it is closely related to the genus Curtobacterium in the class Actinobacteria , showing 96.5–99.9% similarity values to Curtobacterium spp. Phylogenetic analysis based on the gene encoding the gyrase subunit B ( gyr B) and DNA–DNA hybridization suggest that F. oceanosedimentum represents a separate species in the genus Curtobacterium , which is also supported by comparative analysis of cellular fatty acid profiles and a large array of phenotypic traits. We therefore propose to transfer F. oceanosedimentum to the genus Curtobacterium as Curtobacterium oceanosedimentum comb. nov.