Afterword: Thick Time,Heavy Time

ABSTRACT

The paper sums up and comments on the contributions of the Special Issue edited by Katrien Pype and Richard Vokes. The theme of the papers was the impact of new media and radio on life styles and life worlds in Africa with a focus on regions of postcolonial Africa: Congo DRC.     

Association analyses of repeated measures on triglyceride and high-density lipoprotein levels: insights from GAW20

Background

The GAW20 group formed on the theme of methods for association analyses of repeated measures comprised 4sets of investigators. The provided “real” data set included genotypes obtained from a human whole-genome association study based on longitudinal measurements of triglycerides (TGs) and high-density lipoprotein in addition to methylation levels before and after administration of fenofibrate. The simulated data set contained 200 replications of methylation levels and posttreatment TGs, mimicking the real data set.

Results

The different investigators in the group focused on the statistical challenges unique to family-based association analyses of phenotypes measured longitudinally and applied a wide spectrum of statistical methods such as linear mixed models, generalized estimating equations, and quasi-likelihood–based regression models. This article discusses the varying strategies explored by the group’s investigators with the common goal of improving the power to detect association with repeated measures of a phenotype.

Conclusions

Although it is difficult to identify a common message emanating from the different contributions because of the diversity in the issues addressed, the unifying theme of the contributions lie in the search for novel analytic strategies to circumvent the limitations of existing methodologies to detect genetic association.

     

Clean SEA-HSQC: a method to map solvent exposed amides in large non-deuterated proteins with gradient-enhanced HSQC

The recent introduction of the SEA-TROSY experiment (Pellecchia et al. (2001) J. Am. Chem. Soc., 123, 4633–4634) can alleviate the problem of resonance overlap in ¹⁵N/²H labeled proteins. This method selectively observes solvent exposed amide protons with a SEA element. However, SEA-TROSY spectra may be contaminated with exchange-relayed NOE contributions from fast exchanging hydroxyl or amine protons and longitudinal relaxation contributions. Furthermore, for non-deuterated proteins or protein-ligand complexes, SEA-TROSY spectra may contain NOE contributions from aliphatic protons. In this communication, a modified version of the SEA element, a Clean SEA element, is introduced to eliminate these artifacts.     

Stories,fun and games: Teaching genetics in primary school

Nuggets are suggestions with practical advice to help in communicating biology to students. They are shorter than the formal papers and have not been peer-reviewed, but may provide ideas for the classroom. Please send contributions to the editor at: jbe@iob.org     

Decline in Coronary Mortality in Sweden between 1986 and 2002: Comparing Contributions from Primary and Secondary Prevention

BackgroundThe relative importance of risk factor reduction in healthy people (primary prevention) versus that in patients with coronary heart disease (secondary prevention) has been debated. We aimed to quantify the contribution of the two.MethodologyWe used the previously validated IMPACT model to estimate contributions from primary prevention (reducing risk factors in the population, particularly smoking, cholesterol and systolic blood pressure) and from secondary prevention (reducing risk factors in coronary heart disease patients) in the Swedish population.ConclusionsThe largest effects on mortality came from primary prevention, giving markedly larger mortality reductions than secondary prevention.     

Ways to get work done: a review and systematisation of simplification practices in the LCA literature

Purpose

Within the field of life cycle assessment (LCA), simplifications are a response to the practical restrictions in the context of a study. In the 1990s, simplifications were part of a debate on streamlining within LCA. Since then, many studies have been published on simplifying LCA but with little attention to systematise the approaches available. Also, despite being pervasive during the making of LCA studies, simplifications remain often invisible in the final results. This paper therefore reviews the literature on simplification in LCA in order to systematise the approaches found today.

Methods

A review of the LCA simplification literature was conducted. The systematic search and selection process led to a sample of 166 publications. During the review phase, the conceptual contributions to the simplification discourse were evaluated. A dataset of 163 entries was created, listing the conceptual contributions to the simplification debate. An empirically grounded analysis led to the generative development of a systematisation of simplifications according to their underlying simplifying logic.

Results and discussion

Five simplifying logics were identified: exclusion, inventory data substitution, qualitative expert judgment, standardisation and automation. Together, these simplifying logics inform 13 simplification strategies. The identified logics represent approaches to handle the complexities of product systems and expectations of the users of LCA results with the resources available to the analyst. Each simplification strategy is discussed with regard to its main applications and challenges.

Conclusions

This paper provides a first systematisation of the different simplification logics frequently applied in LCA since the original streamlining discussion. The presented terminology can help making communication about simplification more explicit and transparent, thus important for the credibility of LCA. Despite the pervasiveness of simplification in LCA, there is a relative lack of research on simplification per se, making further research describing simplification as a practice and analysing simplifications methodologically desirable.

     

Monocyte subsets and monocyte-platelet aggregates: implications in predicting septic mortality among surgical critical illness patients

Background: Monocyte subsets and monocyte–platelet aggregates (MPAs) play important roles in inflammation. Aim: To evaluate the association between the three human monocyte subsets and their contributions to MPAs and mortality among septic patients. Methods: Consecutive septic patients were enrolled in. Age- and gender-matched nonseptic patients were recruited as control patients. Monocyte subsets and monocyte–platelet aggregates were determined by flow cytometric analysis. Results: Elevated percentage of MPAs (MPAs%) was associated with an increased risk of mortality. Conclusions: This study demonstrated increased MPAs% enables the identification of a group of septic patients at high risk of death.     

Kilovoltage beam model for flat panel imaging system with bow-tie filter for scatter prediction and correction

PurposeKilovoltage flat-panel imaging systems are used for cone-beam Computed Tomography (CBCT) and digital Tomosynthesis (DTS). Hereby, the presence of scatter and relatively large dose from imaging are challenging factors. In this study a phenomenological beam model was developed to characterize imager response to imaging beams with a bow-tie filter (Varian OBI system).Materials and methodThe kilovoltage beam model was based on dose ratio formalism and thus was using standard concepts of megavoltage dose calculation such as scatter factors, tissue maximum ratio and off-axis ratio. Primary and scatter (head and phantom scatter) were modeled with three Gaussian kernels. Parameters were based on measured transmission images for slabs of solid water of different total thickness and various jaw settings.ResultsThe beam model was used to evaluate contributions from primary, secondary and tertiary contributions for different geometrical objects such as cylinders and step-like phantoms. Theoretical predictions of radiographs using the model for known objects are consistent with the measurements.ConclusionSecondary and tertiary contributions were interpreted as scatter and can be subtracted from CBCT projections based on the analytical model. Therefore our model can provide a basis for improvement of image quality (less artifacts due to scatter, better contrast and resolution) in CBCT reconstruction.     

柴达木盆地尕斯库勒盐湖区邻近水体对湖泊微生物群落的贡献

【目的】探究尕斯库勒盐湖生态系统中邻近水体对湖泊微生物的贡献。【方法】采集尕斯库勒盐湖区湖水、沉积物以及邻近的泉水、河水和盐田的水样,对其进行地球化学分析;通过16S rRNA基因的Illumina MiSeq高通量测序分析样品的微生物群落组成。【结果】尕斯库勒盐湖区水体和沉积物中的优势门是变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、放线菌门(Actinobacteria)和广古菌门(Euryarchaeota)。盐度和pH是影响尕斯库勒盐湖区群落组成的最主要环境因素。邻近水体对湖泊水体和沉积物的贡献分别为12.94%和7.53%。【结论】邻近水体对尕斯库勒盐湖微生物群落的贡献有限。     

Un caso di identità tra fasci conduttori alterni radicali e fasci conduttori sovrapposti cotiledonari

Abstract

A survey of all the 154 scientific publications of Emilio Battaglia (1917–2011) is presented, grouped in three main research interests – plant embryology, cytogenetics in plants and cytological terminology – plus other less relevant contributions. Battaglia's past and present role in these disciplines is briefly discussed, in the light of current research on these topics, partly reviewed also in other contributions of the present Plant Biosystems issue.     

Epigenetics,heritability and longitudinal analysis

Background

Longitudinal data and repeated measurements in epigenome-wide association studies (EWAS) provide a rich resource for understanding epigenetics. We summarize 7 analytical approaches to the GAW20 data sets that addressed challenges and potential applications of phenotypic and epigenetic data. All contributions used the GAW20 real data set and employed either linear mixed effect (LME) models or marginal models through generalized estimating equations (GEE). These contributions were subdivided into 3 categories: (a) quality control (QC) methods for DNA methylation data; (b) heritability estimates pretreatment and posttreatment with fenofibrate; and (c) impact of drug response pretreatment and posttreatment with fenofibrate on DNA methylation and blood lipids.

Results

Two contributions addressed QC and identified large statistical differences with pretreatment and posttreatment DNA methylation, possibly a result of batch effects. Two contributions compared epigenome-wide heritability estimates pretreatment and posttreatment, with one employing a Bayesian LME and the other using a variance-component LME. Density curves comparing these studies indicated these heritability estimates were similar. Another contribution used a variance-component LME to depict the proportion of heritability resulting from a genetic and shared environment. By including environmental exposures as random effects, the authors found heritability estimates became more stable but not significantly different. Two contributions investigated treatment response. One estimated drug-associated methylation effects on triglyceride levels as the response, and identified 11 significant cytosine-phosphate-guanine (CpG) sites with or without adjusting for high-density lipoprotein. The second contribution performed weighted gene coexpression network analysis and identified 6 significant modules of at least 30 CpG sites, including 3 modules with topological differences pretreatment and posttreatment.

Conclusions

Four conclusions from this GAW20 working group are: (a) QC measures are an important consideration for EWAS studies that are investigating multiple time points or repeated measurements; (b) application of heritability estimates between time points for individual CpG sites is a useful QC measure for DNA methylation studies; (c) drug intervention demonstrated strong epigenome-wide DNA methylation patterns across the 2 time points; and (d) new statistical methods are required to account for the environmental contributions of DNA methylation across time. These contributions demonstrate numerous opportunities exist for the analysis of longitudinal data in future epigenetic studies.

     

Genetic and Environmental Contributions to Facial Morphological Variation: A 3D Population-Based Twin Study

IntroductionFacial phenotype is influenced by genes and environment; however, little is known about their relative contributions to normal facial morphology. The aim of this study was to assess the relative genetic and environmental contributions to facial morphological variation using a three-dimensional (3D) population-based approach and the classical twin study design.ResultsHeritability of 13 uPC and 17 sPC reached statistical significance, with h² ranging from 38.8% to 78.5% in the former and 30.5% to 84.8% in the latter group. Also, 1222 distances showed evidence of genetic control. Common environment contributed to one PC in both groups and 53 linear distances (4.3%). Unique environment contributed to 17 uPC and 20 sPC and 1245 distances.ConclusionsGenetic factors can explain more than 70% of the phenotypic facial variation in facial size, nose (width, prominence and height), lips prominence and inter-ocular distance. A few traits have shown potential dominant genetic influence: the prominence and height of the nose, the lower lip prominence in relation to the chin and upper lip philtrum length. Environmental contribution to facial variation seems to be the greatest for the mandibular ramus height and horizontal facial asymmetry.     

Lipohypertrophy and Insulin: An Old Dog That Needs New Tricks

ObjectiveTo review the current status of practical knowledge related to insulin-associated lipohypertrophy (LH) — an accumulation of fatty subcutaneous nodules commonly caused by repeated injections and/or infusions of insulin into the same site.MethodsReview of published literature with additional contributions from leading multidisciplinary experts with the emphasis on clinical aspects including pathophysiology, clinical and economic consequences, diagnosis, prevention and treatment.ResultsLH is the most common dermatologic complication of insulin therapy. Risk factors for the development of lipohypertrophy include repeated delivery of large amounts of insulin into the same location over time, repeated injection trauma to the skin and subcutaneous tissue, and multiple injections using the same needle. Subcutaneous insulin injection in skin areas with lipohypertrophy is associated with reduced pain; however, this problem can interfere with insulin absorption, thereby increasing the likelihood of glucose variability, hypo- and hyperglycemia when a site is changed. Modern visualization technology of the subcutaneous space with ultrasound can demonstrate lipohypertrophy early in the course of its development.ConclusionsThe physiological and psychological consequences of developing insulin lipohypertrophy can be prevented and treated with education focusing on insulin injection techniques.     

Benthic insects and fish of the Doubs River system: typological traits and the development of a species continuum in a theoretically extrapolated watercourse

Using the distribution patterns of benthic insects (198 species) and fishes ( 29 species) from 11 tributaries and the main channel of the Doubs River drainage basin (French Jura), the authors have tried to establish whether there is an organization of species into discrete, identifiable communities. Principal Component Analysis (PCA) was used to identify whether a continuum existed, and also used to select 50 least-disturbed sites, which were used to define a theoretical watercourse. The density classes of each species were projected on this longitudinal gradient and each species response was characterised by two typological traits: its typological preferendum (tp) and its typological amplitude (ta),thus creating a synthesis of ecological characteristics. In the typological index given in the appendix, the 210 species which form a biological templet are listed in alphabetical order with their tp and ta values. These typological species traits are useful contributions to a database for running waters biomonitoring.     

Relationship between postural stability and fall risk in elderly people with lumbar spondylosis during local vibratory stimulation for proprioception: a retrospective study

Abstract

Purpose: Reduced proprioception affects fall risks in elderly people with lumbar spondylosis. The decrease in proprioception in the trunk or lower legs may contribute to a decline in postural stability. We aimed to investigate the association between proprioceptive postural stability and fall risks in elderly individuals with lumbar spondylosis.

Materials and Methods: In this retrospective study, the centre-of-pressure displacement was determined in elderly individuals with lumbar spondylosis during upright stance while standing on a Wii Balance Board with their eyes closed (fall-risk group, n?=?55; non-fall-risk group, n?=?60). Vibratory stimulations at 30?Hz were applied to the lumbar multifidus and gastrocnemius to evaluate the relative contributions of proprioceptive signals used in postural control (relative proprioceptive weighting ratio).

Results: Compared with the non-fall-risk group, the fall-risk group displayed a high relative proprioceptive weighting ratio (p?=?0.024). Relative proprioceptive weighting ratio (odds ratio, 1.1; 95% confidence interval: 1.004–1.109) was independently associated with fall risks after adjusting for confounding factors. Among variables related to fall risk, the relative proprioceptive weighting ratio was a significant factor (p?<?0.035).

Conclusion: The fall-risk group of elderly individuals with lumbar spondylosis was dependent on the ankle strategy. The fall risk in elderly people with lumbar spondylosis could be due to over-dependence on the input from muscle spindles in the gastrocnemius.     

Introduction to the special issue: racialized bordering discourses on European Roma

ABSTRACT

In the introduction to this special issue, we briefly introduce everyday bordering as the theoretical framing for the papers and explore its relationship to the process of racialization. We introduce our situated intersectional approach to the study of everyday bordering, illustrating the importance of capturing the differentially situated gazes of a range of social actors. We then go on to contextualize the importance of this framing and approach in a wider discussion of Roma in Europe before concluding with a summary of the particular contributions of each of the papers in this special issue to these debates.     

Serum creatine is not a reliable marker of muscular fitness in young adults

Purpose: Elevated serum creatine and higher handgrip strength are individually associated with better health profiles yet the link between two variables remains unknown. In this cross-sectional study, we evaluated serum creatine levels in relation to handgrip strength in a cohort of 130 young healthy adults (61 women and 69 men; age 23.3?±?2.6?years), while controlling for age, gender, fat-free mass and biomarkers of creatine metabolism as effect modifiers.

Materials and methods: Serum creatine, creatinine and guanidinoacetic acid (GAA) levels were measured with liquid chromatography-tandem mass spectroscopy, while handgrip strength was assessed with a hydraulic hand dynamometer.

Results: Hierarchical multiple regression revealed that our model as a whole explained 79.9% of the variance in handgrip strength (p?p?p?>?0.05).

Conclusions: Having higher blood creatine appears to be unrelated with better physical performance in young healthy adults. Serum creatine was not a reliable marker of muscular fitness in this population.     

Parental behaviour of Spanish Imperial Eagles Aquila adalberti: sexual differences in a moderately dimorphic raptor

Capsule The sexes make significantly different contributions in the tasks of nest-building, incubation and food provisioning to chicks.

Aims To determine the division of parental activities during breeding (nest-building, incubation, brooding, food provisioning and feeding).

Methods Between 1991 and 1998 focal observations were made at nests using 20–60× telescopes. During the incubation period, 11 pairs were studied involving a total of 2812 observation hours over 269 days. During the chick-rearing period, seven pairs were studied involving a total of 5499 observation hours spread over 503 days. The birds were sexed and identified individually on the basis of size, position during copulation, vocalization and plumage differences.

Results Significant differences were found between the sexes in parental behaviour. Males scarcely participated in incubation and contributed significantly more than the females only in food provisioning, both during incubation (food transfers to feed the female) and during chick-rearing (to feed the chicks). Females were responsible for most of the incubation, nest-building (during incubation and chick-rearing), brooding, shading and feeding of chicks. Nest attendance by females decreased over time. In both sexes, food provisioning increased with brood size.

Conclusion Intersexual differences are discussed in the context of the reversed sexual size dimorphism and parental investment strategies. We suggest that in Spanish Imperial Eagles reversed sexual size dimorphism is best explained by the prey capture difficulty hypothesis, than by parental role division during reproduction.     

Protein dynamics in solution and powder measured by incoherent elastic neutron scattering: the influence of Q-range and energy resolution

Incoherent elastic neutron scattering (IENS) has been widely used to measure intramolecular atomic mean square displacements (MSDs) of proteins in powder and in solution. The instrumental energy resolution and the wave vector transfer (Q-range) determine, respectively, the time and length scales of observable motions. In order to investigate contributions of diffusive motions to MSDs measured by this method, we calculated the elastic intensity for several simple scattering functions. We showed that continuous translational diffusion contributes to MSDs in a Q-range where the energy width of the scattering function is of the order of the instrumental energy resolution. We discuss the choice of instruments adapted to focus on intramolecular motions in the presence of solvent or global macromolecular diffusion. The concepts developed are applied to interpret experimental data from H₂O- and D₂O-hydrated proteins. Finally, analogies between the Gaussian approximation in IENS and the Guinier approximation in small-angle scattering are discussed.     

Intermolecular Potential Functions for Adsorption in Zeolites: State of the Art and Effective Models

Abstract

In the simulation of physical adsorption, the adsorbate-adsorbent potential function plays a central role. Much labour is involved in obtaining a potential function which takes into account two-body and three-body dispersion terms in place of a more empirical effective potential, and it is important to enquire whether effective potentials can furnish an acceptable solution to the problem. Here we review the construction of a more elaborate potential function for the interaction of non-polar probes with silicalite and with AlPO₄-5, and analyze the contributions which arise from the different terms. The possibility of employing effective potentials based on the summation of 12–6 or 6-exp functions is examined, and it is concluded that no guarantee can be offered for the success of the simplified procedure.