Adequacy of Visually Classified Particle Count Statistics From Regional Stream Habitat Surveys1

Abstract: Streamlined sampling procedures must be used to achieve a sufficient sample size with limited resources in studies undertaken to evaluate habitat status and potential management‐related habitat degradation at a regional scale. At the same time, these sampling procedures must achieve sufficient precision to answer science and policy‐relevant questions with an acceptable and statistically quantifiable level of uncertainty. In this paper, we examine precision and sources of error in streambed substrate characterization using data from the Environmental Monitoring and Assessment Program (EMAP) of the U.S. Environmental Protection Agency, which uses a modified “pebble count” method in which particle sizes are visually estimated rather than measured. While the coarse (2?) size classes used in EMAP have little effect on the precision of estimated geometric mean (D_gm) or median (D₅₀) particle diameter, variable classification bias among observers can contribute as much as 0.3?, or about 15‐20%, to the root‐mean‐square error (RMSE) of D_gm or D₅₀ estimates. D_gm and D₅₀ estimates based on EMAP data are nearly equal when fine sediments (<2 mm) are excluded, but otherwise can differ by up to a factor of 2 or more, with D_gm < D₅₀ for gravel‐bed streams. The RMSE of reach‐scale particle size estimates based on visually classified particle count data from EMAP surveys, including variability associated with reoccupying unmarked sample reaches during revisits, is up to five to seven times higher than that reported for traditional measured pebble counts by multiple observers at a plot scale. Nonetheless, a variance partitioning analysis shows that the ratio of among site to revisit variance for several EMAP substrate metrics exceeds 8 for many potential regions of interest, suggesting that the data have adequate precision to be useful in regional assessments of channel morphology, habitat quality, or ecological condition.     

All-in-one whole exome sequencing strategy with simultaneous copy number variant,single nucleotide variant and absence-of-heterozygosity analysis in fetuses with structural ultrasound anomalies: A 1-year experience

Objective

We performed a 1-year evaluation of a novel strategy of simultaneously analyzing single nucleotide variants (SNVs), copy number variants (CNVs) and copy-number-neutral Absence-of-Heterozygosity from Whole Exome Sequencing (WES) data for prenatal diagnosis of fetuses with ultrasound (US) anomalies and a non-causative QF-PCR result.

Methods

After invasive diagnostics, whole exome parent-offspring trio-sequencing with exome-wide CNV analysis was performed in pregnancies with fetal US anomalies and a non-causative QF-PCR result (WES-CNV). On request, additional SNV-analysis, restricted to (the) requested gene panel(s) only (with the option of whole exome SNV-analysis afterward) was performed simultaneously (WES-CNV/SNV) or as rapid SNV-re-analysis, following a normal CNV analysis.

Results

In total, 415 prenatal samples were included. Following a non-causative QF-PCR result, WES-CNV analysis was initially requested for 74.3% of the chorionic villus (CV) samples and 45% of the amniotic fluid (AF) samples. In case WES-CNV analysis did not reveal a causative aberration, SNV-re-analysis was requested in 41.7% of the CV samples and 17.5% of the AF samples. All initial analyses could be finished within 2 weeks after sampling. For SNV-re-analysis during pregnancy, turn-around-times (TATs) varied between one and 8 days.

Conclusion

We show a highly efficient all-in-one WES-based strategy, with short TATs, and the option of rapid SNV-re-analysis after a normal CNV result.     

Occupational Health Care in Small and Medium-Sized Enterprises—How Many Doctors Do We Need and How Do We Ensure Good Care?

The translation of the framework directive 89/391/EEC (Council Directive 89/391/EEC) into national law aims at supplying occupational protection and health care to all employees of large, small, and medium-sized enterprises (SMEs) likewise, depending on assessed exposure. Prior incomplete protection of the German workforce with bias against the SMEs requires an assessment of quantitative and qualitative adequacy of present occupational health care practice and also of future needs.

Therefore, the Federal Institute for Occupational Safety and Health of Germany initiated a study to evaluate the present state of occupational health care in 4 regions with different geographic and economic structure. Based on these data the future demand for adequately trained occupational physicians will be estimated by employing a statistical method that allows for including a large number of modifying variables (economic development, demographic change, etc.).

Expected result of the applied technique are the estimated minimal and maximal number of occupational physicians that have to be trained to meet future demand. In the same study models of best practice will be identified and evaluated for general application. The project started in October 1997 and will be finished by January 2000.     

The time of concentration application in studies around the world: a review

Environmental Science and Pollution Research - The time of concentration (Tc) is the main hydrological parameter used to characterize the response of a given Hydrological Response Unit (HRU) to a...     

Farmers’ Attitude Towards Animal Welfare Aspects and Their Practice in Organic Dairy Calf Rearing: a Case Study in Selected Nordic Farms

In organic philosophy, the concept of “naturalness” is of major importance. According to the organic interpretation of animal welfare, natural living is considered a precondition for accomplishing welfare and the principal aims of organic production include the provision of natural living conditions for animals. However, respective regulations are lacking in organic legislation. In practice, the life of a calf in organic rearing systems can deviate from being natural, since common practices in dairy farms include early weaning, dehorning, or cow-calf separation soon after birth. This case study explores how calf welfare is approached in six different organic dairy farms and how far the concept of naturalness is implemented. The farms included in this study were located in Norway and Sweden. A semi-structured questionnaire was used for data collection. The interviewed farmers approach the concept of welfare in various ways and state that “naturalness” is an aspect of animal welfare. However, in practice in the calf rearing systems under study, only a few “naturalness” aspects were implemented. Reasons for the observed discrepancy might lie in differing understandings of “naturalness,” in economic restrictions, and in other trade-offs resulting from production system inherent characteristics and in limited regulation concerning provision of natural living aspects.