Improved methods for measuring forest landscape structure: LiDAR complements field-based habitat assessment

Conservation and monitoring of forest biodiversity requires reliable information about forest structure and composition at multiple spatial scales. However, detailed data about forest habitat characteristics across large areas are often incomplete due to difficulties associated with field sampling methods. To overcome this limitation we employed a nationally available light detection and ranging (LiDAR) remote sensing dataset to develop variables describing forest landscape structure across a large environmental gradient in Switzerland. Using a model species indicative of structurally rich mountain forests (hazel grouse Bonasa bonasia), we tested the potential of such variables to predict species occurrence and evaluated the additional benefit of LiDAR data when used in combination with traditional, sample plot-based field variables. We calibrated boosted regression trees (BRT) models for both variable sets separately and in combination, and compared the models’ accuracies. While both field-based and LiDAR models performed well, combining the two data sources improved the accuracy of the species’ habitat model. The variables retained from the two datasets held different types of information: field variables mostly quantified food resources and cover in the field and shrub layer, LiDAR variables characterized heterogeneity of vegetation structure which correlated with field variables describing the understory and ground vegetation. When combined with data on forest vegetation composition from field surveys, LiDAR provides valuable complementary information for encompassing species niches more comprehensively. Thus, LiDAR bridges the gap between precise, locally restricted field-data and coarse digital land cover information by reliably identifying habitat structure and quality across large areas.

Comparison of gingival crevicular fluid sampling methods in patients with severe chronic periodontitis

The analysis of samplings from periodontal pockets is important in the diagnosis and therapy of periodontitis. In this study, three different sampling techniques were compared to determine whether one method yielded samples suitable for the reproducible and simultaneous determination of bacterial load, cytokines, neutrophil elastase, and arginine-specific gingipains (Rgps). Rgps are an important virulence factor of Porphyromonas gingivalis, the exact concentration of which in gingival crevicular fluid (GCF) has not been quantified.

Circulating matrix metalloproteinase 9 levels in relation to sampling methods, femoral and carotid atherosclerosis.

OBJECTIVES To examine whether circulating levels of matrix metalloproteinase 9 (MMP-9) were associated with ultrasound-assessed intima-media thickness (IMT) and echolucent plaques in the carotid and femoral arteries. To examine preanalytical sources of variability in MMP-9 concentrations related to sampling procedures. SUBJECTS AND DESIGN Plasma and serum MMP-9 levels were compared with ultrasound assessed measures of femoral and carotid atherosclerosis, in a cross-sectional study of 61-year-old men (n = 473). Preanalytical sources of variability in MMP-9 levels were examined in 10 healthy subjects. Main outcome measures were circulating levels of MMP-9 in serum and plasma, IMT of the carotid and femoral arteries, and plaque status based on size and echolucency. SETTING Research unit at university hospital. RESULTS Plasma concentrations of total and active MMP-9 were associated with femoral artery IMT independently of traditional cardiovascular risk factors, and were higher in subjects with moderate to large femoral plaques. Plasma MMP-9 concentration was higher in men with echolucent femoral plaques (P = 0.006) compared with subjects without femoral plaques. No similar associations were found for carotid plaques. MMP-9 concentrations were higher in serum than in plasma, and higher when sampling was performed with Vacutainer than with syringe. MMP-9 levels in serum were more strongly associated with peripheral neutrophil count compared with MMP-9 levels in plasma. CONCLUSIONS Plasma MMP-9 levels were associated with atherosclerosis in the femoral artery, and total MMP-9 concentration was higher in men with echolucent femoral plaques. The choice of sample material and sampling method affect the measurements of circulating MMP-9 levels.

Comparison of bacterial plaque samples from titanium implant and tooth surfaces by different methods

Studies have shown similarities in the microflora between titanium implants or tooth sites when samples are taken by gingival crevicular fluid (GCF) sampling methods. The purpose of the present study was to study the microflora from curette and GCF samples using the checkerboard DNA-DNA hybridization method to assess the microflora of patients who had at least one oral osseo-integrated implant and who were otherwise dentate. Plaque samples were taken from tooth/implant surfaces and from sulcular gingival surfaces with curettes, and from gingival fluid using filter papers. A total of 28 subjects (11 females) were enrolled in the study. The mean age of the subjects was 64.1 years (SD+/-4.7). On average, the implants studied had been in function for 3.7 years (SD+/-2.9). The proportion of Streptococcus oralis (P<0.02) and Fusobacterium periodonticum (P<0.02) was significantly higher at tooth sites (curette samples). The GCF samples yielded higher proportions for 28/40 species studies (P-values varying between 0.05 and 0.001). The proportions of Tannerella forsythia (T. forsythensis), and Treponema denticola were both higher in GCF samples (P<0.02 and P<0.05, respectively) than in curette samples (implant sites). The microbial composition in gingival fluid from samples taken at implant sites differed partly from that of curette samples taken from implant surfaces or from sulcular soft tissues, providing higher counts for most bacteria studied at implant surfaces, but with the exception of Porphyromonas gingivalis. A combination of GCF and curette sampling methods might be the most representative sample method.

Standard methods for Nosema research

Methods are described for working with Nosema apis and Nosema ceranae in the field and in the laboratory. For fieldwork, different sampling methods are described to determine colony level infections at a given point in time, but also for following the temporal infection dynamics. Suggestions are made for how to standardise field trials for evaluating treatments and disease impact. The laboratory methods described include different means for determining colony level and individual bee infection levels and methods for species determination, including light microscopy, electron microscopy, and molecular methods (PCR). Suggestions are made for how to standardise cage trials, and different inoculation methods for infecting bees are described, including control methods for spore viability. A cell culture system for in vitro rearing of Nosema spp. is described. Finally, how to conduct different types of experiments are described, including infectious dose, dose effects, course of infection and longevity tests

Understanding deforestation and forest fragmentation from a livelihood perspective

Worldwide, forests provide a wide variety of resources to rural inhabitants, and especially to the poor. In Madagascar, forest resources make important contributions to the livelihoods of the rural population living at the edges of these forests. Although people benefit from forest resources, forests are continuously cleared and converted into arable land. Despite long-term efforts on the part of researchers, development cooperation projects and government, Madagascar has not been able to achieve a fundamental decrease in deforestation. The question of why deforestation continues in spite of such efforts remains. To answer this question, we aimed at understanding deforestation and forest fragmentation from the perspective of rural households in the Manompana corridor on the east coast. Applying a sustainable livelihood approach, we explored local social-ecological systems to understand: (i) how livelihood strategies leading to deforestation evolve and (ii) how the decrease of forest impacts on households' strategies. Results highlight the complexity of the environmental, cultural and political context in which households’ decision-making takes place. Further, we found crucial impacts of deforestation and forest fragmentation on livelihood systems, but also recognized that people have been able to adapt to the changing landscapes without major impacts on their welfare.

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.

Biovolatilisation: a poorly studied pathway of the arsenic biogeochemical cycle

It has been known for over a hundred years that microorganisms can produce volatile arsenic (As) species, termed “arsines”. However, this topic has received relatively little attention compared to As behaviour in soils and biotransformation through the trophic level in the marine and terrestrial environment. We believe this is due to long-standing misconceptions regarding volatile As stability and transport as well as an absence, until recently, of appropriate sampling methods. First and foremost, an attempt is made to unify arsines' designations, notations and formulas, taking into account all the different terms used in the literature. Then, the stability of As volatile species is discussed and new analytical developments are explored. Further, the special cases of diffuse low-level emissions (e.g. soil and sediment biovolatilisation), and point sources with high-level emissions (geothermal environments, landfills, and natural gas) are comprehensively reviewed. In each case, future possible areas of research and unknown mechanisms are identified and their importance towards the global As biogeochemical cycle is explored. This review gathers new information regarding mechanisms, stability, transport and sampling of the very elusive arsines and shows that more research should be conducted on this important process.

Design of nest access grids and perches in front of the nests: Influence on the behavior of laying hens.

In aviary systems for laying hens, it is important to provide suitable nest access platforms in front of the nests, allowing hens to reach and explore each of the nests easily. This access platform is needed to achieve good nest acceptance by the hens and thereby prevent mislaid eggs. In the present experiment, the behavior of hens using 2 different nest access platforms, a plastic grid and 2 wooden perches, was examined. Furthermore, the nests were placed on both sides of the aviary rack (corridor side and outdoor side), either integrated into the aviary rack itself (integrated nest; IN) or placed on the walls of the pens (wall nest; WN), resulting in a 2 × 2 factorial design Four thousand five hundred white laying hens were housed in 20 test pens. The eggs in the nests and mislaid eggs were collected daily, and the behavior of hens on the nest accesses was filmed during wk 25 and 26, using focal observation and scan sampling methods. More balancing, body contact, and agonistic interactions were expected for nests with perches, whereas more walking and nest inspections were expected for nests with grids. There were more mislaid eggs and balancing found in pens equipped with nests with wooden perches. More agonistic interactions and balancing, less standing, and a longer duration of nest inspection were found with the WN compared with the IN. Interactions between platform design and position of the nests were found for duration of nest visits, body contact, and walking, with the highest amount for WN equipped with plastic grids. Nests on the corridor side were favored by the hens. Nest-related behaviors, such as nest inspection, standing, and walking, decreased over time as did the number of hens on the nest accesses, whereas sitting increased. These results indicate that the hens had more difficulties in gripping the perches as designed. The lower number of hens on the nest access platforms in front of IN may be due to a better distribution around nests and tier changes within the aviary rack. Based on these results, grids rather than perches provide for improved nesting behavior.

Geochemical synthesis for the Effingen Member in boreholes at Oftringen, Gösgen and Küttigen

The Effingen Member is a low-permeability rock unit of Oxfordian age (ca. 160 Ma) that occurs across northern Switzerland. It comprises sandy calcareous marls and (argillaceous) limestones. This report describes the hydrogeochemistry, mineralogy and supporting physical properties of the Effingen Member in three boreholes in the Jura-Südfuss area: Oftringen, Gösgen and Küttigen, where it is 220–240 m thick. The top of the Effingen Member is at 420, 66 and 32 m depths at the three sites. Core materials are available from Oftringen and Gösgen, whereas information from Küttigen is limited to cuttings, in-situ hydrogeological testing and geophysical logging. Hydrogeological boundaries of the Effingen Member vary between locations. Ground-water flows were identified during drilling at the top (Geissberg Member), but not at the base, of the Effingen Member at Oftringen, at the base (Hauptrogenstein Formation) of the Effingen Member at Gösgen, and in a limestone layer (Gerstenhübel unit) within the Effingen Member at Küttigen. The marls and limestones of the Effingen Member have carbonate contents of 46–91 wt.-% and clay-mineral contents of 5–37 wt.-%. Pyrite contents are up to 1.6 wt.-%, but no sulphate minerals were detected by routine analyses. Clay minerals are predominantly mixed-layer illite-smectite, illite and kaolinite, with sporadic traces of chlorite and smectite. Veins filled with calcite ± celestite occur through the Effingen Member at Oftringen but not at Gösgen or Küttigen. They formed at 50–70 ºC from externally derived fluids, probably of Miocene age. Water contents are 0.7–4.2 wt.-%, corresponding to a water-loss porosity range of 1.9–10.8 vol.-%. Specific surface areas, measured by the BET method, are 2–30 m2/g, correlating with clay-mineral contents. Water activity has been measured and yielded surprisingly low values down to 0.8. These cannot be explained by pore-water salinity alone and include other effects, such as changes in the fabric due to stress release or partial saturation. Observed variations in measurements are not fully understood. Cation exchange capacity (CEC) and exchangeable cation populations have been studied by the Ni-en method. CEC, derived from the consumption of the index cation Ni, is 9–99 meq/kgrock at a solid:liquid ratio of 1, correlating with the clay-mineral content. Cation concentrations in Ni-en extract solutions are in the order Na+≥Ca2+>Mg2+>K+>Sr2+. However, the analytical results from the Ni-en extractions have additional contributions from cations originating from pore water and from mineral dissolution reactions that occurred during extraction, and it was not possible to reliably quantify these contributions. Therefore, in-situ cation populations and selectivity coefficients could not be derived. A suite of methods have been used for characterising the chemical compositions of pore waters in the Effingen Member. Advective displacement was used on one sample from each Oftringen and Gösgen and is the only method that produces results that approach complete hydrochemical compositions. Aqueous extraction was used on core samples from these two boreholes and gives data only for Cl- and, in some cases, Br-. Out-diffusion was used on core samples from Oftringen and similarly gives data for Cl- and Br- only. For both aqueous extraction and out-diffusion, reaction of the experimental water with rock affected concentrations of cations, SO42 and alkalinity in experimental solutions. Another method, centrifugation, failed to extract pore water. Stable isotope ratios (δ18O and δ2H) of pore waters in core samples from Oftringen were analysed by the diffusive exchange method and helium contents of pore water in Oftringen samples were extracted for mass spectrometric analysis by quantitative outgassing of preserved core samples. Several lines of evidence indicate that drillcore samples might not have been fully saturated when opened and subsampled in the laboratory. These include comparisons of water-loss porosities with physical porosities, water-activity measurements, and high contents of dissolved gas as inferred from ground-water samples. There is no clear proof of partial saturation and it is unclear whether this might represent in-situ conditions or is due to exsolution of gas due to the pressure release since drilling. Partial saturation would have no impact on the recalculation of pore-water compositions from aqueous extraction experiments using water-loss porosity data. The largest uncertainty in the pore-water Cl- concentrations recalculated from aqueous extraction and out-diffusion experiments is the magnitude of the anion-accessible fraction of water-loss porosity. General experience of clay-mineral rich formations suggests that the anion-accessible porosity fraction is very often about 0.5 and generally in a range of 0.3 to 0.6 and tends to be inversely correlated with clay-mineral contents. Comparisons of the Cl- concentration in pore water obtained by advective displacement with that recalculated from aqueous extraction of an adjacent core sample suggests a fraction of 0.27 for an Oftringen sample, whereas the same procedure for a Gösgen sample suggests a value of 0.64. The former value for anion-accessible porosity fraction is presumed to be unrepresentative given the local mineralogical heterogeneity at that depth. Through-diffusion experiments with HTO and 36Cl- suggest that the anion-accessible porosity fraction in the Effingen Member at Oftringen and Gösgen is around 0.5. This value is proposed as a typical average for rocks of the Effingen Member, bearing in mind that it varies on a local scale in response to the heterogeneity of lithology and pore-space architecture. The substantial uncertainties associated with the approaches to estimating anion-accessible porosity propagate into the calculated values of in-situ pore-water Cl- concentrations. On the basis of aqueous extraction experiments, and using an anion-accessible porosity fraction of 0.5, Cl- concentrations in the Effingen Member at Oftringen reach a maximum of about 14 g/L in the centre. Cl- decreases upwards and downwards from that, forming a curved depth profile. Cl- contents in the Effingen Member at Gösgen increase with depth from about 3.5 g/L to about 14 g/L at the base of the cored profile (which corresponds to the centre of the formation). Out-diffusion experiments were carried out on four samples from Oftringen, distributed through the Effingen Member. Recalculated Cl- concentrations are similar to those from aqueous extraction for 3 out of the 4 samples, and somewhat lower for one sample. Concentrations of other components, i.e. Na+, K+, Ca2+, Mg2+, Sr2+, SO42- and HCO3- cannot be obtained from the aqueous extraction and out-diffusion experimental data because of mineral dissolution and cation exchange reactions during the experiments. Pore-water pH also is not constrained by those extraction experiments. The only experimental approach to obtain complete pore-water compositions for samples from Oftringen and Gösgen is advective displacement of pore water. The sample from Oftringen used for this experiment is from 445 m depth in the upper part of the Effingen Member and gave eluate with 16.5 g/L Cl- whereas aqueous extraction from a nearby sample indicated about 9 g/L Cl-. The sample from Gösgen used for advective displacement is from 123 m depth in the centre of the Effingen Member sequence and gave eluate with about 9 g/L Cl- whereas aqueous extraction gave 11.5 g/L Cl-. In both cases the pore waters have Na-(Ca)-Cl compositions and SO42- concentrations of about 1.1 g/L. The Gösgen sample has a Br/Cl ratio similar to that of sea water, whereas this ratio is lower for the Oftringen sample. Taking account of uncertainties in the applied experimental approaches, it is reasonable to place an upper limit of ca. 20 g/L on Cl- concentration for pore water in the Effingen Member in this area. There are major discrepancies between pore-water SO42- concentrations inferred from aqueous extraction or out-diffusion experiments and those obtained from advective displacement in both the Oftringen and Gösgen cases. A general conclusion is that all or at least part of the discrepancies are attributable to perturbation of the sulphur system and enhancement of SO42- by sulphate mineral dissolution and possibly minor pyrite oxidation during aqueous extraction and out-diffusion. Therefore, data for SO42- calculated from those pore-water sampling methods are considered not to be representative of in-situ conditions. A reference pore-water composition was defined for the Effingen Member in the Jura Südfuss area. It represents the probable upper limits of Cl- contents and corresponding anion and cation concentrations that are reasonably constrained by experimental data. Except for Cl- and possibly Na+ concentrations, this composition is poorly constrained especially with respect to SO42- and Ca2+ concentrations, and pH and alkalinity. Stable isotope compositions, δ18O and δ2H, of pore waters in the Effingen Member at Oftringen plot to the right of the meteoric water line, suggesting that 18O has been enriched by water-rock exchange, which indicates that the pore waters have a long residence time. A long residence time of pore water is supported by the level of dissolved 4He that has accumulated in pore water of the Effingen Member at Oftringen. This is comparable with, or slightly higher than, the amounts of 4He in the Opalinus Clay at Benken. Ground waters were sampled from flowing zones intersected by boreholes at the three locations. The general interpretation is that pore waters and ground-water solutes may have similar origins in Mesozoic and Cenozoic brackish-marine formations waters, but ground-water solutes have been diluted rather more than pore waters by ingress of Tertiary and Quaternary meteoric waters. The available hydrochemical data for pore waters from the Effingen Member at these three locations in the Jura-Südfuss area suggest that the geochemical system evolved slowly over geological periods of time, in which diffusion was an important mechanism of solute transport. The irregularity of Cl- and δ18O profiles and spatial variability of advective ground-water flows in the Malm-Dogger system suggests that palaeohydrogeological and hydrochemical responses to changing tectonic and surface environmental conditions were complex.

The basel cocktail for simultaneous phenotyping of human cytochrome P450 isoforms in plasma, saliva and dried blood spots.

BACKGROUND AND OBJECTIVE Phenotyping cocktails use a combination of cytochrome P450 (CYP)-specific probe drugs to simultaneously assess the activity of different CYP isoforms. To improve the clinical applicability of CYP phenotyping, the main objectives of this study were to develop a new cocktail based on probe drugs that are widely used in clinical practice and to test whether alternative sampling methods such as collection of dried blood spots (DBS) or saliva could be used to simplify the sampling process. METHODS In a randomized crossover study, a new combination of commercially available probe drugs (the Basel cocktail) was tested for simultaneous phenotyping of CYP1A2, CYP2B6, CYP2C9, CYP2C19, CYP2D6 and CYP3A4. Sixteen subjects received low doses of caffeine, efavirenz, losartan, omeprazole, metoprolol and midazolam in different combinations. All subjects were genotyped, and full pharmacokinetic profiles of the probe drugs and their main metabolites were determined in plasma, dried blood spots and saliva samples. RESULTS The Basel cocktail was well tolerated, and bioequivalence tests showed no evidence of mutual interactions between the probe drugs. In plasma, single timepoint metabolic ratios at 2 h (for CYP2C19 and CYP3A4) or at 8 h (for the other isoforms) after dosing showed high correlations with corresponding area under the concentration-time curve (AUC) ratios (AUC0-24h parent/AUC0-24h metabolite) and are proposed as simple phenotyping metrics. Metabolic ratios in dried blood spots (for CYP1A2 and CYP2C19) or in saliva samples (for CYP1A2) were comparable to plasma ratios and offer the option of minimally invasive or non-invasive phenotyping of these isoforms. CONCLUSIONS This new combination of phenotyping probe drugs can be used without mutual interactions. The proposed sampling timepoints have the potential to facilitate clinical application of phenotyping but require further validation in conditions of altered CYP activity. The use of DBS or saliva samples seems feasible for phenotyping of the selected CYP isoforms.

Factors controlling decomposition rates of fine root litter in temperate forests and grasslands

Background and aims Fine root decomposition contributes significantly to element cycling in terrestrial ecosystems. However, studies on root decomposition rates and on the factors that potentially influence them are fewer than those on leaf litter decomposition. To study the effects of region and land use intensity on fine root decomposition, we established a large scale study in three German regions with different climate regimes and soil properties. Methods In 150 forest and 150 grassland sites we deployed litterbags (100 μm mesh size) with standardized litter consisting of fine roots from European beech in forests and from a lowland mesophilous hay meadow in grasslands. In the central study region, we compared decomposition rates of this standardized litter with root litter collected on-site to separate the effect of litter quality from environmental factors. Results Standardized herbaceous roots in grassland soils decomposed on average significantly faster (24 ± 6 % mass loss after 12 months, mean ± SD) than beech roots in forest soils (12 ± 4 %; p < 0.001). Fine root decomposition varied among the three study regions. Land use intensity, in particular N addition, decreased fine root decomposition in grasslands. The initial lignin:N ratio explained 15 % of the variance in grasslands and 11 % in forests. Soil moisture, soil temperature, and C:N ratios of soils together explained 34 % of the variance of the fine root mass loss in grasslands, and 24 % in forests. Conclusions Grasslands, which have higher fine root biomass and root turnover compared to forests, also have higher rates of root decomposition. Our results further show that at the regional scale fine root decomposition is influenced by environmental variables such as soil moisture, soil temperature and soil nutrient content. Additional variation is explained by root litter quality.

Simulating Carbon Stocks and Fluxes of an African Tropical Montane Forest with an Individual-Based Forest Model

Tropical forests are carbon-dense and highly productive ecosystems. Consequently, they play an important role in the global carbon cycle. In the present study we used an individual-based forest model (FORMIND) to analyze the carbon balances of a tropical forest. The main processes of this model are tree growth, mortality, regeneration, and competition. Model parameters were calibrated using forest inventory data from a tropical forest at Mt. Kilimanjaro. The simulation results showed that the model successfully reproduces important characteristics of tropical forests (aboveground biomass, stem size distribution and leaf area index). The estimated aboveground biomass (385 t/ha) is comparable to biomass values in the Amazon and other tropical forests in Africa. The simulated forest reveals a gross primary production of 24 tcha-1yr-1. Modeling above- and belowground carbon stocks, we analyzed the carbon balance of the investigated tropical forest. The simulated carbon balance of this old-growth forest is zero on average. This study provides an example of how forest models can be used in combination with forest inventory data to investigate forest structure and local carbon balances.

Working Alliance Inventory-Short Revised (WAI-SR): psychometric properties in outpatients and inpatients

The Working Alliance Inventory-Short Revised (WAI-SR) is a recently refined measure of the therapeutic alliance that assesses three key aspects of the therapeutic alliance: (a) agreement on the tasks of therapy, (b) agreement on the goals of therapy and (c) development of an affective bond. The WAI-SR demonstrated good psychometric properties in an initial validation in psychotherapy outpatients in the USA. The generalizability of these findings is limited because in some countries a substantial portion of individual psychotherapy is delivered in inpatient settings. This study investigated and compared the psychometric properties of the WAI-SR in German outpatients (N = 88) and inpatients (N = 243). In both samples reliability (alpha > 0.80) and convergent validity with the Helping Alliance Questionnaire were good (r > 0.64). Confirmatory factor analysis showed acceptable to good model fit for the proposed Bond-Task-Goal model in both samples. Multi-group analysis demonstrated that the same constructs were measured across settings. Alliance ratings of outpatients and inpatients differed regarding the overlap of alliance components and the magnitude of the alliance ratings: The differentiation of the alliance components was poorer in inpatients and they reported lower alliances. Unique aspects of the alliance in inpatient treatment are discussed and a need for further research on the alliance in inpatient settings is pointed out. Overall, the WAI-SR can be recommended for alliance assessment in both settings.