The physical map of {\it Escherichia coli\/} K-12 strain MG1655: Construction, comparison with other strains and implications for mechanisms controlling oligonucleotide frequency

Complete NotI, SfiI, XbaI and BlnI cleavage maps of Escherichia coli K-12 strain MG1655 were constructed. Techniques used included: CHEF pulsed field gel electrophoresis; transposon mutagenesis; fragment hybridization to the ordered $\lambda$ library of Kohara et al.; fragment and cosmid hybridization to Southern blots; correlation of fragments and cleavage sites with EcoMap, a sequence-modified version of the genomic restriction map of Kohara et al.; and correlation of cleavage sites with DNA sequence databases. In all, 105 restriction sites were mapped and correlated with the EcoMap coordinate system.^ NotI, SfiI, XbaI and BlnI restriction patterns of five commonly used E. coli K-12 strains were compared to those of MG1655. The variability between strains, some of which are separated by numerous steps of mutagenic treatment, is readily detectable by pulsed-field gel electrophoresis. A model is presented to account for the difference between the strains on the basis of simple insertions, deletions, and in one case an inversion. Insertions and deletions ranged in size from 1 kb to 86 kb. Several of the larger features have previously been characterized and some of the smaller rearrangements can potentially account for previously reported genetic features of these strains.^ Some aspects of the frequency and distribution of NotI, SfiI, XbaI and BlnI cleavage sites were analyzed using a method based on Markov chain theory. Overlaps of Dam and Dcm methylase sites with XbaI and SfiI cleavage sites were examined. The one XbaI-Dam overlap in the database is in accord with the expected frequency of this overlap. The occurrence of certain types of SfiI-Dcm overlaps are overrepresented. Of the four subtypes of SfiI-Dcm overlap, only one has a partial inhibitory effect on the activity of SfiI. Recognition sites for all four enzymes are rarer than expected based on oligonucleotide frequency data, with this effect being much stronger for XbaI and BlnI than for NotI and SfiI. The latter two enzyme sites are rare mainly due to apparent negative selection against GGCC (both) and CGGCCG (NotI). The former two enzyme sites are rare mainly due to effects of the VSP repair system on certain di-tri- and tetranucleotides, most notably CTAG. Models are proposed to explain several of the anomalies of oligonucleotide distribution in E. coli, and the biological significance of the systems that produce these anomalies is discussed. ^

Characteristics, Distribution and Persistence of Thin Layers Over a 48 Hour Period

The biological and physical processes contributing to planktonic thin layer dynamics were examined in a multidisciplinary study conducted in East Sound, Washington, USA between June 10 and June 25, 1998. The temporal and spatial scales characteristic of thin layers were determined using a nested sampling strategy utilizing 4 major types of platforms: (1) an array of 3 moored acoustical instrument packages and 2 moored optical instrument packages that recorded distributions and intensities of thin layers; (2) additional stationary instrumentation deployed outside the array comprised of meteorological stations, wave-tide gauges, and thermistor chains; (3) a research vessel anchored 150 m outside the western edge of the array; (4) 2 mobile vessels performing basin-wide surveys to define the spatial extent of thin layers and the physical hydrography of the Sound. We observed numerous occurrences of thin layers that contained locally enhanced concentrations of material; many of the layers persisted for intervals of several hours to a few days. More than one persistent thin layer may be present at any one time, and these spatially distinct thin layers often contain distinct plankton assemblages. The results suggest that the species or populations comprising each distinct thin layer have responded to different sets of biological and/or physical processes. The existence and persistence of planktonic thin layers generates extensive biological heterogeneity in the water column and may be important in maintaining species diversity and overall community structure.

Climate change in Switzerland: a review of physical, institutional, and political aspects

Climate change is clearly discernible in observed climate records in Switzerland. It impacts on natural systems, ecosystems, and economic sectors such as agriculture, tourism, and energy, and it affects Swiss livelihood in various ways. The observed and projected changes call for a response from the political system, which in Switzerland is characterized by federalism and direct democratic instruments. Swiss climate science embraces natural and social sciences and builds on institutionalized links between researchers, public, and private stakeholders. In this article, we review the physical, institutional, and political aspects of climate change in Switzerland. We show how the current state of Swiss climate science and policy developed over the past 20 years in the context of international developments and national responses. Specific to Switzerland is its topographic setting with mountain regions and lowlands on both sides of the Alpine ridge, which makes climate change clearly apparent and for some aspects (tourist sector, hydropower, and extreme events) highly relevant and better perceivable (e.g., retreating glaciers). Not surprisingly the Alpine region is of central interest in Swiss climate change studies.

International Clostridium difficile animal strain collection and large diversity of animal associated strains

BACKGROUND Clostridium difficile is an important cause of intestinal infections in some animal species and animals might be a reservoir for community associated human infections. Here we describe a collection of animal associated C. difficile strains from 12 countries based on inclusion criteria of one strain (PCR ribotype) per animal species per laboratory. RESULTS Altogether 112 isolates were collected and distributed into 38 PCR ribotypes with agarose based approach and 50 PCR ribotypes with sequencer based approach. Four PCR ribotypes were most prevalent in terms of number of isolates as well as in terms of number of different host species: 078 (14.3% of isolates; 4 hosts), 014/020 (11.6%; 8 hosts); 002 (5.4%; 4 hosts) and 012 (5.4%; 5 hosts). Two animal hosts were best represented; cattle with 31 isolates (20 PCR ribotypes; 7 countries) and pigs with 31 isolates (16 PCR ribotypes; 10 countries). CONCLUSIONS This results show that although PCR ribotype 078 is often reported as the major animal C. difficile type, especially in pigs, the variability of strains in pigs and other animal hosts is substantial. Most common human PCR ribotypes (014/020 and 002) are also among most prevalent animal associated C. difficile strains worldwide. The widespread dissemination of toxigenic C. difficile and the considerable overlap in strain distribution between species furthers concerns about interspecies, including zoonotic, transmission of this critically important pathogen.

Regional differences of physical activity and sedentary behaviour in Swiss children are not explained by socio-demographics or the built environment

Objective We evaluated whether regional differences in physical activity (PA) and sedentary behaviour (SB) existed along language boundaries within Switzerland and whether potential differences would be explained by socio-demographics or environmental characteristics. Methods We combined data of 611 children aged 4 to 7 years from four regional studies. PA and SB were assessed by accelerometers. Information about the socio-demographic background was obtained by questionnaires. Objective neighbourhood attributes could be linked to home addresses. Multivariate regression models were used to test associations between PA and SB and socio-demographic characteristics and neighbourhood attributes. Results Children from the German compared to the French-speaking region were more physically active and less sedentary (by 10–15 %, p < 0.01). Although German-speaking children lived in a more favourable environment and a higher socioeconomic neighbourhood (differences p < 0.001), these characteristics did not explain the differences in PA behaviour between French and German speaking. Conclusions Factors related to the language region, which might be culturally rooted were among the strongest correlates of PA and SB among Swiss children, independent of individual, social and environmental factors.

Dyadic action control in overweight and obese couples: Effectiveness of a randomized controlled trial to promote physical activity.

BACKGROUND: Enhancing physical activity in overweight and obese individuals is an important means to promote health in this target population. The Health Action Process Approach (HAPA), which was the theoretical framework of this study, focuses on individual self-regulation variables for successful health behavior change. One key self-regulation variable of this model is action control with its three subfacets awareness of intentions, self-monitoring and regulatory effort. The social context of individuals, however, is usually neglected in common health behavior change theories. In order to integrate social influences into the HAPA, this randomized controlled trial investigated the effectiveness of a dyadic conceptualization of action control for promoting physical activity. METHODS/DESIGN: This protocol describes the design of a single-blind randomized controlled trial, which comprises four experimental groups: a dyadic action control group, an individual action control group and two control groups. Participants of this study are overweight or obese, heterosexual adult couples who intend to increase their physical activity. Blocking as means of a gender-balanced randomization is used to allocate couples to conditions and partners to either being the target person of the intervention or to the partner condition. The ecological momentary intervention takes place in the first 14 days after baseline assessment and is followed by another 14 days diary phase without intervention. Follow-ups are one month and six months later. Subsequent to the six-months follow-up another 14 days diary phase takes place.The main outcome measures are self-reported and accelerometer-assessed physical activity. Secondary outcome measures are Body Mass Index (BMI), aerobic fitness and habitual physical activity. DISCUSSION: This is the first study examining a dyadic action control intervention in comparison to an individual action control condition and two control groups applying a single-blind randomized control trial. Challenges with running couples studies as well as advantages and disadvantages of certain design-related decisions are discussed. This RCT was funded by the Swiss National Science Foundation (PP00P1_133632/1) and was registered on 27/04/2012 at http://www.isrctn.com/ISRCTN15705531.

A review of air–ice chemical and physical interactions (AICI): liquids, quasi-liquids, and solids in snow

Snow in the environment acts as a host to rich chemistry and provides a matrix for physical exchange of contaminants within the ecosystem. The goal of this review is to summarise the current state of knowledge of physical processes and chemical reactivity in surface snow with relevance to polar regions. It focuses on a description of impurities in distinct compartments present in surface snow, such as snow crystals, grain boundaries, crystal surfaces, and liquid parts. It emphasises the microscopic description of the ice surface and its link with the environment. Distinct differences between the disordered air–ice interface, often termed quasi-liquid layer, and a liquid phase are highlighted. The reactivity in these different compartments of surface snow is discussed using many experimental studies, simulations, and selected snow models from the molecular to the macro-scale. Although new experimental techniques have extended our knowledge of the surface properties of ice and their impact on some single reactions and processes, others occurring on, at or within snow grains remain unquantified. The presence of liquid or liquid-like compartments either due to the formation of brine or disorder at surfaces of snow crystals below the freezing point may strongly modify reaction rates. Therefore, future experiments should include a detailed characterisation of the surface properties of the ice matrices. A further point that remains largely unresolved is the distribution of impurities between the different domains of the condensed phase inside the snowpack, i.e. in the bulk solid, in liquid at the surface or trapped in confined pockets within or between grains, or at the surface. While surface-sensitive laboratory techniques may in the future help to resolve this point for equilibrium conditions, additional uncertainty for the environmental snowpack may be caused by the highly dynamic nature of the snowpack due to the fast metamorphism occurring under certain environmental conditions. Due to these gaps in knowledge the first snow chemistry models have attempted to reproduce certain processes like the long-term incorporation of volatile compounds in snow and firn or the release of reactive species from the snowpack. Although so far none of the models offers a coupled approach of physical and chemical processes or a detailed representation of the different compartments, they have successfully been used to reproduce some field experiments. A fully coupled snow chemistry and physics model remains to be developed.

Risk factors for borderline personality disorder in treatment seeking patients with a substance use disorder: an international multicenter study

Borderline personality disorder (BPD) and substance use disorders (SUDs) often co-occur, partly because they share risk factors. In this international multicenter study, risk factors for BPD were examined for SUD patients. In total, 1,205 patients were comprehensively examined by standardized interviews and questionnaires on psychiatric diagnosis and risk factors, and it was found that 1,033 (85.7%) had SUDs without BPD (SUD) and 172 (14.3%) had SUD with BPD (SUD + BPD). SUD + BPD patients were significantly younger, more often females and more often diagnosed with comorbid adult attention deficit/hyperactivity disorder. SUD + BPD patients did not differ from SUD patients on most risk factors typical for SUD such as maternal use of drugs during pregnancy or parents having any SUD. However, SUD + BPD patients did have a higher risk of having experienced emotional and physical abuse, neglect, or family violence in childhood compared to SUD patients, suggesting that child abuse and family violence are BPD-specific risk factors in patients with SUDs. © 2015 S. Karger AG, Basel.

Sampling in Open Source Software Development: The case for using the Debian GNUILinux Distribution

Research on open source software (OSS) projects often focuses on the SourceForge collaboration platform. We argue that a GNU/Linwr distribution, such as Debian, is better suited for the sampling ofprojects because it avoids biases and contains unique information only available in an integrated environment. Especially research on the reuse of components can build on dependency information inherent in the Debian GNU/Linux packaging system. This paper therefore contributes to the practice of sampling methods in OSS research and provides empirical data on reuse dependencies in Debian.

Relative Age Effect in Young Swiss Alpine Skiers From 2004 to 2011

PURPOSE To verify whether the relative age effects (RAEs) occur among young male and female Swiss alpine skiers of different age groups and performance levels. Additionally, the efficacy of normalizing performance in physical tests to height and body mass to attenuate RAEs eventually present was tested. METHODS The Swiss-Ski Power Test consists of anthropometric measures and physical tests for coordination and speed, endurance and strength and is used since 2004 to evaluate 11- to 19-years old Swiss competitive alpine skiers. We analysed the distribution of 6996 tests performed by 1438 male and 1031 female alpine skiers between 2004 and 2011 according to the athlete's relative age quartile (Q). Differences in anthropometric measures and performance in physical tests according to Q were assessed and the possibility of attenuating eventual RAEs on performance by normalization of results to height and body mass was tested. RESULTS RAEs were found among all female and male age groups, with no differences between age groups. While performance level did not affect RAE for male skiers, it influenced RAE among female skiers. RAEs also influenced results in all physical tests except upper limbs strength. Normalization of results to body mass attenuated most RAEs identified. CONCLUSION small RAEs are present among young Swiss competitive alpine skiers and should be taken into account in training and selection settings, avoiding the waste of possible future talents. When ranking junior athletes according to their performance in physical tests, normalization of results to body mass decreases the bias caused by RAEs.