Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.     

Strategies for defining traits when calculating economic values for livestock breeding: a review

The objective of the present review was (i) to survey different approaches for choosing the complex of traits for which economic values (EVs) are calculated, (ii) to call attention to the proper definition of traits and (iii) to discuss the manner and extent to which relationships among traits have been considered in the calculation of EVs. For this purpose, papers dealing with the estimation of EVs of traits in livestock were reviewed. The most important reasons for incompatibility of EVs for similar traits estimated in different countries and by different authors were found to be inconsistencies in trait definitions and in assumptions being made about relationships among traits. An important problem identified was how to choose the most appropriate criterion to characterise production or functional ability for a particular class of animals. Accordingly, the review covered the following three topics: (i) which trait(s) would best characterise the growth ability of an animal; (ii) how to define traits expressed repeatedly in subsequent reproductive cycles of breeding females and (iii) how to deal with traits that differ in average value between sexes or among animal groups. Various approaches that have been used to solve these problems were discussed. Furthermore, the manner in which diverse authors chose one or more traits from a group of alternatives for describing a specific biological potential were reviewed and commented on. The consequences of including or excluding relationships among economically important traits when estimating the EV for a specific trait were also examined. An important conclusion of the review is that, for a better comparability and interpretability of estimated EVs in the literature, it is desirable that clear and unique definitions of the traits, complete information on assumptions used in analytical models and details on inter-relationships between traits are documented. Furthermore, the method and the model used for the genetic evaluation of specific traits in a certain breeding organisation are important for the exact definition of traits, for which the economic values will be calculated, and for the inclusion or exclusion of relationships among traits in the calculation of the EVs in livestock breeding.     

Reliability of map accuracy assessments: A reply to Roff et al. (2016)

Roff et al. (Ecological Management and Restoration, 17 , 2016, 000) provide a discussion of the criteria expected for the best approach to validation of mapping programs and uses Hunter (Ecological Management & Restoration 17 , 2016, 40) to highlight issues involved. While we support the general principles outlined, we note that the review does not apply the same standards to Sivertsen et al. (Greater Hunter Native Vegetation Mapping Geodatabase Guide (Version 4.0). Office of Environment and Heritage, Department of the Premier and Cabinet, Sydney, Australia, 2011), the original document critiqued by Hunter (Ecological Management & Restoration 17 , 2016, 40). The Hunter (Ecological Management & Restoration 17 , 2016, 40) validation was based on a larger sample size, greater sampling within mapping units and greater representation of landscapes than Sivertsen et al. (Greater Hunter Native Vegetation Mapping Geodatabase Guide (Version 4.0). Office of Environment and Heritage, Department of the Premier and Cabinet, Sydney, Australia, 2011). Survey and validation sites being placed along public roads and lands are common to both the general Office of Environment and Heritage (OEH) and Hunter (Ecological Management & Restoration 17 , 2016, 40) validation methodologies. Thus, the criticisms of Roff et al. (Ecological Management and Restoration, 17 , 2016, 000) of the Hunter (Ecological Management & Restoration 17 , 2016, 40) approach apply equally, if not more, to Sivertsen et al. (Greater Hunter Native Vegetation Mapping Geodatabase Guide (Version 4.0). Office of Environment and Heritage, Department of the Premier and Cabinet, Sydney, Australia, 2011). We outline in the article how the Roff et al. (Ecological Management and Restoration, 17 , 2016, 000) critique was selective and in some cases incorrect in its analysis of issues presented in Hunter (Ecological Management & Restoration 17 , 2016, 40) and did not apply the same criteria to their own work. We conclude by discussing future directions for validating and mapping vegetation communities.     

Time to wake up: No impact of COMT Val158Met gene variation on circadian preferences,arousal regulation and sleep

Dopamine has been implicated in the regulation of sleep–wake states and the circadian rhythm. However, there is no consensus on the impact of two established dopaminergic gene variants: the catechol-O-methyltransferase Val158Met (COMT Val158Met; rs4680) and the dopamine D4 receptor Exon III variable-number-of-tandem-repeat polymorphism (DRD4 VNTR). Pursuing a multi-method approach, we examined their potential effects on circadian preferences, arousal regulation and sleep. Subjects underwent a 7-day actigraphy assessment (SenseWear Pro3), a 20-minute resting EEG (analyzed using VIGALL 2.0) and a body mass index (BMI) assessment. Further, they completed the Morningness–Eveningness Questionnaire (MEQ), the Epworth Sleepiness Scale (ESS) and the Pittsburgh Sleep Quality Index (PSQI). The sample comprised 4625 subjects (19–82 years) genotyped for COMT Val158Met, and 689 elderly subjects (64–82 years) genotyped for DRD4 VNTR. The number of subjects varied across phenotypes. Power calculations revealed a minimum required phenotypic variance explained by genotype ranging between 0.5% and 1.5% for COMT Val158Met and between 3.3% and 6.0% for DRD4 VNTR. Analyses did not reveal significant genotype effects on MEQ, ESS, PSQI, BMI, actigraphy and EEG variables. Additionally, we found no compelling evidence in sex- and age-stratified subsamples. Few associations surpassed the threshold of nominal significance (p < .05), providing some indication for a link between DRD4 VNTR and daytime sleepiness. Taken together, in light of the statistical power obtained in the present study, our data particularly suggest no impact of the COMT Val158Met polymorphism on circadian preferences, arousal regulation and sleep. The suggestive link between DRD4 VNTR and daytime sleepiness, on the other hand, might be worth investigation in a sample enriched with younger adults.     

文化景观作为区域景观研究概念——德国图林根州文化景观研究、教学与规划实践

近20 年来,对风景园林的文化阐释成为埃尔夫特应用科技大学文化景观研究组持续以来的关注焦点。期间,该研究组系统地分析了决定图林根州文化景观的各种文化因素和要素,深入了解文化和自然环境中的复杂相互作用,以此来表述和研究图林根州的区域景观系统。首先,阐述了当下德国风景园林学术语境中“文化景观”的含义,强调文化对于景观质量的价值。继而,论述了对景观进行优化、保护和设计中无法否定和回避的文化与经济因素。这样既要发展经济又要保护文化的矛盾性质,是文化景观概念所理解的人类生存的重要性质所在。文化景观研究能够在看似统一的地理区域中,形成和发展为具有可识别性的、差异化的动态结构。此外,文化景观研究还涉及其他因素,诸如生物多样性与文化多样性的丧失、生态系统服务功能滞后、经济价值的低估、国土空间连接性以及缺少实质性评价的人文特征。对历史性文化景观价值的认知给风景园林学带来了机遇,对历史景观不仅要保护,而且要创造并提供各种富有成效的展示,以参与文化景观的未来发展。维护和整合风景园林规划设计中文化景观遗产的研究实践,可以通过基础设施项目的环境影响评估到建成区的景观设计整体过程中得以贯彻。更好地理解文化景观,有助于在空间规划和发展中对其更加谨慎地进行处理,以提高文化景观研究的科学和策略意识。     

Expansion of symmetric exon-bordering domains does not explain evolution of lineage specific genes in mammals

In order to examine the evolution of lineage specific genes, we analyzed intron phase distributions and exon-bordering domains in primate and rodent specific genes. We found that the expansion of symmetric exon-bordering domains could not explain the evolution of lineage specific genes. Rather internal intron loss of a domain can partially explain the excess of class 1–1 intron phases in the lineage specific genes. We suggest the event that led to excess of symmetric exons in lineage specific genes had little bearing on shaping the phenotypes specific to the individual lineage. Instead, Kruppel-associated box (KRAB) proteins associated with zinc finger C2H2 (zf-C2H2) type are likely to be responsible for the lineage specific function.     

Probable blind spot in the International Diabetes Federation definition of metabolic syndrome

Objectives: The International Diabetes Federation (IDF) proposed a novel definition of the metabolic syndrome (MS) in 2005, which designated central obesity as mandatory. The new National Cholesterol Education Program (NCEP) version, announced by the American Heart Association and National Heart Lung and Blood Institute in October 2005, did not favor any of the five components. We set out to compare the cardiovascular profiles of patients cross‐defined by these two definitions to shed light on the differential meanings of the two. Research Methods and Procedures: We analyzed data from 2608 non‐institutionalized adults (≥19 years old) in the National Nutrition and Health Survey in Taiwan, who had complete data for the five MS defining components. Both definitions adopted lower cut‐points for fasting glucose and race‐specific cut‐points for waist circumference. Results: Under the IDF's and new NCEP's definitions, the MS prevalence was 6.2% and 11.6% in men and 12.6% and 16.5% in women, respectively. Although the two definitions had high agreement, IDF failed to pick up ～4% to 5% of people with more than three MS component disorders but a waist circumference less than the cut‐point. Subjects whose physical conditions only satisfied NCEP's definition had similar or worse metabolic profiles than those whose conditions satisfied both IDF's definition and the new NCEP's definition. Discussion: The IDF definition would fail to identify a portion of people who have more than three MS component disorders but a small waistline. Further research and discussion are needed on whether and how to implement the IDF's definition.     

基因外显子连接序列与相应内含子序列的相互作用

剪接后的内含子与相应mRNA序列的相互作用在基因表达调控过程中起着非常重要的作用。基于27个物种的核糖核蛋白基因序列,采用Smith—Waterman局域比对方法得到外显子连接序列与相应内含子序列的最佳匹配片段,分析了外显子连接序列上的匹配频率分布和匹配片段的序列特征。发现一些低等真核生物EJC结合区域的匹配频率明显低于其它区域,所有物种EJC结合区域的序列构成呈现出相对低的结构序。最佳匹配片段的平均长度和配对率分布与siRNA和miRNA的结合特征相同。推测EJC和内含子在与外显子序列结合的过程中存在相互竞争和相互协作的关系,内含子中部序列在基因表达调控过程中起着重要的作用。     

Sequence analysis of an amphioxus cosmid containing a gene homologous to members of the aldo-keto reductase gene superfamily

To gain an insight into vertebrate genome evolution, we have analysed the organization of an approximately 40-kb genomic clone of an amphioxus (Branchiostoma floridae) cosmid library. Amphioxus is considered as being the last non-vertebrate relative to vertebrates. Sequencing and analysis of the above clone using three different exon prediction programs (Grail, GenScan, Mzef) have led to the identification of a gene of the aldo-keto reductase family as well as further exons that gave a significant database match to known genes.