Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement

Molecular data are now widely used in epidemiological studies to investigate the transmission, distribution, biology, and diversity of pathogens. Our objective was to establish recommendations to support good scientific reporting of molecular epidemiological studies to encourage authors to consider specific threats to valid inference. The statement Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) builds upon the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) initiative. The STROME-ID statement was developed by a working group of epidemiologists, statisticians, bioinformaticians, virologists, and microbiologists with expertise in control of infection and communicable diseases. The statement focuses on issues relating to the reporting of epidemiological studies of infectious diseases using molecular data that were not addressed by STROBE. STROME-ID addresses terminology, measures of genetic diversity within pathogen populations, laboratory methods, sample collection, use of molecular markers, molecular clocks, timeframe, multiple-strain infections, non-independence of infectious-disease data, missing data, ascertainment bias, consistency between molecular and epidemiological data, and ethical considerations with respect to infectious-disease research. In total, 20 items were added to the 22 item STROBE checklist. When used, the STROME-ID recommendations should advance the quality and transparency of scientific reporting, with clear benefits for evidence reviews and health-policy decision making.

Family Preservation Journal, 1998, Volume 3, Issue 1. (Entire issue)

Entire issue (large pdf file) Articles include: The Role of Consistency and Diversity in Building Knowledge in Family Preservation. Debora J. Cavazos Dylla and Marianne Berry The Weekly Adjustment Indicators Checklist: An Application in the Child Welfare Field. Michael H. Epstein, Madhavi Jayanthi, Janet McKelvey, Deborah Holderness, Erin Frankenberry, Cassandra Lampkin, Molly McGrath, and Kari White Intensive Family Preservation Services: a Short History but a Long Past. Kellie B. Reed and Raymond S. Kirk Collaborative Conversations for Change: A Solution-Focused Approach to Family Centered Practice. Donald F. Fausel

Molecular analysis of the human $\gamma$-chain T cell receptor genes

In our studies we have focused on the issue of variability and diversity of the $\gamma$ (or $\delta)$ chain T cell receptor (TCR) genes by studying cDNA transcripts in peripheral blood mononuclear cells or $\gamma\delta$ TCR+ T cell clones. The significance of these studies lies in the better understanding of the molecular biology of the $\gamma\delta$ T cell receptor as well as in answering the question whether certain molecular forms predominate in $\gamma\delta$ T cells exhibiting specific immunologic functions. We establish that certain $\gamma$-chain TCR genes exhibit particular patterns of rearrangements in cDNA transcripts in normal individuals. V$\gamma$I subgroup were shown to preferentially rearrange to J$\gamma$2C$\gamma$2 gene segments. These preferential VJC rearrangements, may have implications regarding the potential for diversity and polymorphism of the $\gamma$-chain TCR gene. In addition, the preferential association of V$\gamma$I genes with J$\gamma$2C$\gamma$2, which encode a non-disulfide-linked $\gamma\delta$ TCR, suggests that $\gamma$ chains utilizing V$\gamma$I are predominantly expressed as non-disulfide-linked $\gamma\delta$ TCR heterodimers. The implications of this type of expression remain to be determined. We identified two alternative splicing events of the $\gamma$-chain TCR genes occurring in high frequency in all the normal individuals examined. These events may suggest additional mechanisms of regulation and control as well as diversification of $\gamma\delta$ TCR gene expression. The question whether particular forms of $\gamma$ or $\delta$-chain TCR genes are involved in HLA Class I recognition by specific $\gamma\delta$ cytotoxic T cell clones was addressed. Our results indicated that the T cell clones expressed identical $\gamma$ but distinct $\delta$-chains suggesting that the specificity for recognition of HLA-A2 or HLA-A3 may be conferred by the $\delta$-chain TCR. The issue of the degree of diversity and polymorphism of the $\delta$-chain TCR genes in a patient with a primary immunodeficiency (Omenn's syndrome) was addressed. A limited pattern of rearrangements in peripheral blood transcripts was found, suggesting that a limited $\gamma\delta$ TCR repertoire may be expressed in this particular primary immunodeficiency syndrome. Overall, our findings suggest that $\delta$-chain TCR genes exhibit the potential for significant diversity and that there are certain preferential patterns of expression that may be associated with particular immunologic functions. ^

Seasonal controls on grassland microbial biogeography: Are they governed by plants, abiotic properties or both?

Temporal dynamics create unique and often ephemeral conditions that can influence soil microbial biogeography at different spatial scales. This study investigated the relation between decimeter to meter spatial variability of soil microbial community structure, plant diversity, and soil properties at six dates from April through November. We also explored the robustness of these interactions over time. An historically unfertilized, unplowed grassland in southwest Germany was selected to characterize how seasonal variability in the composition of plant communities and substrate quality changed the biogeography of soil microorganisms at the plot scale (10 m x 10 m). Microbial community spatial structure was positively correlated with the local environment, i.e. physical and chemical soil properties, in spring and autumn, while the density and diversity of plants had an additional effect in the summer period. Spatial relationships among plant and microbial communities were detected only in the early summer and autumn periods when aboveground biomass increase was most rapid and its influence on soil microbial communities was greatest due to increased demand by plants for nutrients. Individual properties exhibited varying degrees of spatial structure over the season. Differential responses of Gram positive and Gram negative bacterial communities to seasonal shifts in soil nutrients were detected. We concluded that spatial distribution patterns of soil microorganisms change over a season and that chemical soil properties are more important controlling factors than plant density and diversity. Finer spatial resolution, such as the mm to cm scale, as well as taxonomic resolution of microbial groups, could help determine the importance of plant species density, composition, and growth stage in shaping microbial community composition and spatial patterns. (C) 2014 The Authors. Published by Elsevier Ltd. All rights reserved.

Coprological analyses on apparently healthy Alpine ibex (Capra ibex ibex) from two Swiss colonies

To provide baseline parasitological data for health surveillance in free-ranging Alpine ibex (Capra ibex ibex), we assessed the endoparasite population and level of parasitism in apparently healthy ibex. Faecal samples from 148 ibex were collected between 2006 and 2008 in two different Swiss ibex colonies. They were analysed by coprology, including combined sedimentation/flotation method, sedimentation method, Baermann funnel technique and Ziehl-Neelsen staining. Gastrointestinal parasites and lungworms were identified in 100% and 81.8% of the examined animals, respectively. Highest prevalences were recorded for gastrointestinal strongylids other than Nematodirus/Marshallagia spp. (100%), Eimeria spp. (100%), Muellerius spp. (79.8%) and Nematodirus/Marshallagia spp. (79.0%). We report for the first time Cryptosporidium sp. in free-ranging Alpine ibex and Cystocaulus spp. in free-ranging ibex from Switzerland. On average, ibex were infected with 3.9 different parasites taxa (range: 1-8). Parasite prevalence and diversity varied significantly between sexes, study sites and seasons. Parasite egg output was low in 95.7% and moderate in 5.3% of the samples. Overall, the results indicate that Alpine ibex are widely infected with endoparasites and suggest that multiple infections are very common in apparently healthy populations. Furthermore, our data underline the potential influence of factors such as sex, study site and season on parasitological findings.

Sustainable Wastewater Management: Is it Possible to Regulate Micropollution in the Future by Learning from the Past? A Policy Analysis

This paper applies a policy analysis approach to the question of how to effectively regulate micropollution in a sustainable manner. Micropollution is a complex policy problem characterized by a huge number and diversity of chemical substances, as well as various entry paths into the aquatic environment. It challenges traditional water quality management by calling for new technologies in wastewater treatment and behavioral changes in industry, agriculture and civil society. In light of such challenges, the question arises as to how to regulate such a complex phenomenon to ensure water quality is maintained in the future? What can we learn from past experiences in water quality regulation? To answer these questions, policy analysis strongly focuses on the design and choice of policy instruments and the mix of such measures. In this paper, we review instruments commonly used in past water quality regulation. We evaluate their ability to respond to the characteristics of a more recent water quality problem, i.e., micropollution, in a sustainable way. This way, we develop a new framework that integrates both the problem dimension (i.e., causes and effects of a problem) as well as the sustainability dimension (e.g., long-term, cross-sectoral and multi-level) to assess which policy instruments are best suited to regulate micropollution. We thus conclude that sustainability criteria help to identify an appropriate instrument mix of end-of-pipe and source-directed measures to reduce aquatic micropollution.

Dynamics of the nasal microbiota in infancy: A prospective cohort study.

BACKGROUND Understanding the composition and dynamics of the upper respiratory tract microbiota in healthy infants is a prerequisite to investigate the role of the microbiota in patients with respiratory diseases. This is especially true in early life, when the immune system is in development. OBJECTIVE We sought to describe the dynamics of the upper respiratory tract microbiota in healthy infants within the first year of life. METHODS After exclusion of low-quality samples, microbiota characterization was performed by using 16S rDNA pyrosequencing of 872 nasal swabs collected biweekly from 47 unselected infants. RESULTS Bacterial density increased and diversity decreased within the first year of life (R(2) = 0.95 and 0.73, respectively). A distinct profile for the first 3 months of life was found with increased relative abundances of Staphlyococcaceae and Corynebacteriaceae (exponential decay: R(2) = 0.94 and 0.96, respectively). In addition, relative bacterial abundance and composition differed significantly from summer to winter months. The individual composition of the microbiota changed with increasing time intervals between samples and was best modeled by an exponential function (R(2) = 0.97). Within-subject dissimilarity in a 2-week time interval was consistently lower than that between subjects, indicating a personalized microbiota. CONCLUSION This study reveals age and seasonality as major factors driving the composition of the nasal microbiota within the first year of life. A subject's microbiota is personalized but dynamic throughout the first year. These data are indispensable to interpretation of cross-sectional studies and investigation of the role of the microbiota in both healthy subjects and patients with respiratory diseases. They might also serve as a baseline for future intervention studies.

Stuck in Mobility? Fragmented Journeys of Migrants without Chances of Admission in Europe

This paper is about young migrants without chance of being granted legal residence status in the Schengen zone. Previous observations suggest that some migrants, whose country of origin leaves them with low chances of receiving asylum or in fact any type of residence permit, exhibit a highly complex migration pattern that is characterised by 1) durable “transit” across Europe, which is a multi-linear movement according to opportunities that open up along the journey; 2) a high degree of flexibility, as they have to respond to suddenly changing conditions, such as work opportunities, rejection of asylum claims, detention or deportation, and 3) switching between different legal statuses, such as asylum seeker, sans papiers or detainee. The experiences of these young adults thus show a deep ambivalence between a sense of autonomy, on the one hand, and of profound hope and powerlessness, on the other. The Dublin Convention intends to limit such a hypermobility of migrants but seems to fail in many cases. Simultaneously it provokes some of the movements by sending asylum seekers and irregular migrants back to their first country of arrivals. Given the fact that little is known about these fragmented journeys inside of the Schengen area, this ethnographic study produces novel data on a highly pertinent migration pattern, the impact of the European migration management on individual migrants as well as the inter-relatedness of the asylum regime and irregular migration in Europe. At the same time these fragmented journeys are an excellent example to discuss mobility as a resource on the one hand (since it enables this specific migrant group to extend their presence in Europe) and as a handicap on the other (since it impedes the building of stable social networks, the planning of the future, etc.).

Effects of forest management on bryophyte communities on deadwood

Epixylic bryophytes are important components of forest vegetation but are currently endangered by increment of wood harvest and intensive forest management. In this paper we present a study about the relationship between forest management, deadwood abundance, deadwood attributes and species richness of epixylic bryophytes on 30 plots comprising three forest types (managed coniferous, managed deciduous and unmanaged deciduous forests) in three regions in Germany. Additionally we analyzed the relations between deadwood attributes (wood species, decay, deadwood type, size) and bryophytes on deadwood items (n = 799) and calculated species interaction networks of wood species and bryophytes. Overall, species richness of epixylic bryophytes was positively related to deadwood abundance and diversity. The mean deadwood abundance was lowest in unmanaged forests (9.7 m³ ha^-1) compared with 15.0 m³ ha^-1 in managed deciduous and 25.1 m³ ha^-1 in managed coniferous forests. Accordingly, epixylic bryophyte species richness per plot increased from 7 species per 400 m 2 in unmanaged, 10 in managed deciduous and 16 in managed coniferous forests. The interaction network provided evidence of importance of tree-species diversity for bryophyte diversity and the relevance of particular wood species for rare bryophytes.

Generally, the results demonstrate a considerable lack of deadwood in all forest types, even in unmanaged forests. Species richness of epixylic bryophytes was strongly limited by available substrates within the observed deadwood abundance ranging up to only 60 m³ ha^-1. Altogether, this suggests a high demand to increase both abundance and diversity of deadwood in forests.

Can we infer plant facilitation from remote sensing? a test across global drylands

Facilitation is a major force shaping the structure and diversity of plant communities in terrestrial ecosystems. Detecting positive plant–plant interactions relies on the combination of field experimentation and the demonstration of spatial association between neighboring plants. This has often restricted the study of facilitation to particular sites, limiting the development of systematic assessments of facilitation over regional and global scales. Here we explore whether the frequency of plant spatial associations detected from high-resolution remotely sensed images can be used to infer plant facilitation at the community level in drylands around the globe. We correlated the information from remotely sensed images freely available through Google Earth with detailed field assessments, and used a simple individual-based model to generate patch-size distributions using different assumptions about the type and strength of plant–plant interactions. Most of the patterns found from the remotely sensed images were more right skewed than the patterns from the null model simulating a random distribution. This suggests that the plants in the studied drylands show stronger spatial clustering than expected by chance. We found that positive plant co-occurrence, as measured in the field, was significantly related to the skewness of vegetation patch-size distribution measured using Google Earth images. Our findings suggest that the relative frequency of facilitation may be inferred from spatial pattern signals measured from remotely sensed images, since facilitation often determines positive co-occurrence among neighboring plants. They pave the road for a systematic global assessment of the role of facilitation in terrestrial ecosystems. Read More: http://www.esajournals.org/doi/10.1890/14-2358.1

New developments providing mechanistic insight into the impact of the microbiota on allergic disease

The increase in allergic diseases over the past several decades is correlated with changes in the composition and diversity of the intestinal microbiota. Microbial-derived signals are critical for instructing the developing immune system and conversely, immune regulation can impact the microbiota. Perturbations in the microbiota composition may be especially important during early-life when the immune system is still developing, resulting in a critical window of opportunity for instructing the immune system. This review highlights recent studies investigating the role of the microbiome in susceptibility or development of allergic diseases with a focus on animal models that provide insight into the mechanisms and pathways involved. Identification of a causal link between reduced microbial diversity or altered microbial composition and increased susceptibility to immune-mediated diseases will hopefully pave the way for better preventive therapies.

Investigation of Pliocene foraminifera on sediment core CRP-1 from the Ross Sea, Antarctica

Mixed assemblages of Pliocene and Quaternary foraminifera occur within the Quaternary succession of the CRP-1 drillhole. Pliocene foraminifera are not present in the lowermost Unit 4.1. are rare in Unit 3.1 and 2.3, are relatively common in Units 2.2 and 2.1, and are absent in Unit 1.1. Fifteen and twelve species were documented in two of the samples from Units 2.2 and 2.1 respectively. A census count of foraminifera in a sample at 26.89 mbsf (Unit 2.2) indicated that 39% of the tests were from a Pliocene source, with the remaining 61% tests assigned to the in situ Quaternary assemblage. There appears to be a close correlation between the stratigraphic distribution of ice-rafted sediments and the test number and diversity of Pliocene taxa. It is concluded that Pliocene assemblages were not derived from submarine outcrops on Roberts Ridge, but are more likely to have been rafted to the site via major trunk valley drainage systems such as operated within the Mackay and Ferrar glacial valleys. The co-occurrence of marine biota (including foraminifera), fossil wood, pollen, and igneous clasts in the Quaternary succession of CRP-l, points to the marine and terrestrial facies of the Pliocene Sirius Group as a likely source. A major episode of erosion and transport of sediment into the offshore marine basins at about ~1 Ma may have been triggered by dynamism in the ice sheet-glacier system, an episode of regional uplift in the Transantarctic Mountains, sea level oscillations and associated changes in the land-to-sea drainage baselines, or some combination of these factors.

Ground beetle (Carabidae) abundance data from north-eastern Australian rainforest, between June 2008 - January 2010, using pitfall traps

Understanding how the environment influences patterns of diversity is vital for effective conservation management, especially in a changing global climate. While assemblage structure and species richness patterns are often correlated with current environmental factors, historical influences may also be considerable, especially for taxa with poor dispersal abilities. Mountain-top regions throughout tropical rainforests can act as important refugia for taxa characterised by low dispersal capacities such as flightless ground beetles (Carabidae), an ecologically significant predatory group. We surveyed flightless ground beetles along elevational gradients in five different subregions within the Australian Wet Tropics World Heritage Area to investigate (1) whether the diversity and composition of flightless ground beetles are elevationally stratified, and, if so, (2) what environmental factors (other than elevation per se) are associated with these patterns. Generalised linear models and model averaging techniques were used to relate patterns of diversity to environmental factors. Unlike most taxonomic groups, flightless ground beetles increased in species richness and abundance with elevation. Additionally, each subregion consisted of distinct assemblages containing a high level of regional endemic species. Species richness was most strongly positively associated with the historical climatic conditions and negatively associated with severity of recent disturbance (treefalls) and current climatic conditions. Assemblage composition was associated with latitude and current and historical climatic conditions. Our results suggest that distributional patterns of flightless ground beetles are not only likely to be associated with factors that change with elevation (current climatic conditions), but also factors that are independent of elevation (recent disturbance and historical climatic conditions). Variation in historical vegetation stability explained both species richness and assemblage composition patterns, probably reflecting the significance of upland refugia at a geographic time scale. These findings are important for conservation management as upland habitats are under threat from climate change.

Statistics of the National soil test database of France

In France, farmers commission about 250,000 soil-testing analyses per year to assist them managing soil fertility. The number and diversity of origin of the samples make these analyses an interesting and original information source regarding cultivated topsoil variability. Moreover, these analyses relate to several parameters strongly influenced by human activity (macronutrient contents, pH...), for which existing cartographic information is not very relevant. Compiling the results of these analyses into a database makes it possible to re-use these data within both a national and temporal framework. A database compilation relating to data collected over the period 1990-2009 has been recently achieved. So far, commercial soil-testing laboratories approved by the Ministry of Agriculture have provided analytical results from more than 2,000,000 samples. After the initial quality control stage, analytical results from more than 1,900,000 samples were available in the database. The anonymity of the landholders seeking soil analyses is perfectly preserved, as the only identifying information stored is the location of the nearest administrative city to the sample site. We present in this dataset a set of statistical parameters of the spatial distributions for several agronomic soil properties. These statistical parameters are calculated for 4 different nested spatial entities (administrative areas: e.g. regions, departments, counties and agricultural areas) and for 4 time periods (1990-1994, 1995-1999, 2000-2004, 2005-2009). Two kinds of agronomic soil properties are available: the firs one correspond to the quantitative variables like the organic carbon content and the second one corresponds to the qualitative variables like the texture class. For each spatial unit and temporal period, we calculated the following statistics stets: the first set is calculated for the quantitative variables and corresponds to the number of samples, the mean, the standard deviation and, the 2-,4-,10-quantiles; the second set is calculated for the qualitative variables and corresponds to the number of samples, the value of the dominant class, the number of samples of the dominant class, the second dominant class, the number of samples of the second dominant class.