Phenology of the avian spring migratory passage in Europe and North America : Asymmetric advancement in time and increase in duration

Climate change has been shown to shift the seasonal timing (i.e. phenology) and distribution of species. The phenological effects of climate change on living organisms have often been tested using first occurrence dates, which may be uninformative and biased. More rarely investigated is how different phases of a phenological sequence (e.g. beginning, central tendency and end) or its duration have changed over time. This type of analysis requires continuous observation throughout the phenological event over multiple years, and such data sets are rare. In this study we examined the impact of temperature on long-term change of passage timing and duration of the spring migration period in birds, and which species' traits explain species-specific variation. Data used covered 195 species from 21 European and Canadian bird observatories from which systematic daily sampling protocols were available. Migration dates were negatively associated with early spring temperature and timings had in general advanced in 57 years. Short-distance migrants advanced the beginning of their migration more than long-distance migrants when corrected for phylogenic relatedness, but such a difference was not found in other phases of migration. The advancement of migration has generally been greater for the beginning and median phases of migration relative to the end, leading to extended spring migration seasons. Duration of the migration season increased with increasing temperature. Phenological changes have also been less noticeable in Canada even when corrected for rate of change in temperature. To visualize long-term changes in phenology, we constructed the first multi-species spring migration phenology indicator to describe general changes in median migration dates in the northern hemisphere. The indicator showed an average advancement of one week during five decades across the continents (period 1959-2015). The indicator is easy to update with new data and we therefore encourage future research to investigate whether the trend towards longer periods of occurrence or emergence in spring is also evident in other migratory populations. Such phenological changes may influence detectability in monitoring schemes, and may have broader implications on population and community dynamics.Peer reviewe

Evaluation of [3H]proline for radioautographic tracing of axonal projections in the teleost visual system

The efficacy of [3H]proline radioautography for tracing retinal ganglion cell projections to the optic tectum of the jewel fish, Hemichromis bimaculatus, has been compared with that of degeneration techniques. There was good agreement between the various methods. Retinal projections to the optic tectum of two other teleosts, the oscar, Astronotus ocellatus, and the goldfish, Carrasius auratus, were examined radioautographically.In addition to conventional methods of analysis, radioautograms were scanned in a slit microdensitometer and by an automated isodensity scanning system. Results of studies with the protein synthesis inhibitor, cycloheximide, are compatible with the suggestion that axonally transported proteins labeled with [3H]proline may release diffusible precursors that are reincorporated into protein in adjacent regions.The possible advantages and limitations of radioautography of [3H]proline-labeled axonally transported protein in brief or extended studies are discussed in terms of the results obtained in the teleost visual system.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22035/1/0000453.pd

Missing the Match Might Not Cost You the Game : Primer-Template Mismatches Studied in Different Hepatitis A Virus Variants

Mismatches between template sequences and reverse transcription (RT) or polymerase chain reaction (PCR) primers can lead to underestimation or false negative results during detection and quantification of sequence-diverse viruses. We performed an in silico inclusivity analysis of a widely used RT-PCR assay for detection of hepatitis A virus (HAV) in food, described in ISO 15216-1. One of the most common mismatches found was a single G (primer) to U (template) mismatch located at the terminal 3 '-end of the reverse primer region. This mismatch was present in all genotype III sequences available in GenBank. Partial HAV genomes with common or potentially severe mismatches were produced by in vitro transcription and analysed using RT-ddPCR and RT-qPCR. When using standard conditions for RT-qPCR, the mismatch identified resulted in underestimation of the template concentration by a factor of 1.7-1.8 and an increase in 95% limit of detection from 8.6 to 19 copies/reaction. The effect of this mismatch was verified using full-length viral genomes. Here, the same mismatch resulted in underestimation of the template concentration by a factor of 2.8. For the partial genomes, the presence of additional mismatches resulted in underestimation of the template concentration by up to a factor of 232. Quantification by RT-ddPCR and RT-qPCR was equally affected during analysis of RNA templates with mismatches within the reverse primer region. However, on analysing DNA templates with the same mismatches, we found that ddPCR quantification was less affected by mismatches than qPCR due to the end-point detection technique

A new assay for quantitative detection of hepatitis A virus

Hepatitis A virus (HAV) is mainly transmitted via contaminated food or water or through person-to-person contact. Here, we describe development and evaluation of a reverse transcription droplet digital PCR (RTddPCR) and reverse transcription real-time PCR (RT-qPCR) assay for detection of HAV in food and clinical specimens. The assay was evaluated by assessing limit of detection, precision, matrix effects, sensitivity and quantitative agreement. The 95 % limit of detection (LOD95 %) was 10 % higher for RT-ddPCR than for RTqPCR. A Bayesian model was used to estimate precision on different target concentrations. From this, we found that RT-ddPCR had somewhat greater precision than RT-qPCR within runs and markedly greater precision between runs. By analysing serum from naturally infected persons and a naturally contaminated food sample, we found that the two methods agreed well in quantification and had comparable sensitivities. Tests with artificially contaminated food samples revealed that neither RT-ddPCR nor RT-qPCR was severely inhibited by presence of oysters, raspberries, blueberries or leafy-green vegetables. For this assay, we conclude that RT-qPCR should be considered if rapid, qualitative detection is the main interest and that RT-ddPCR should be considered if precise quantification is the main interest. The high precision of RT-ddPCR allows for detection of small changes in viral concentration over time, which has direct implications for both food control and clinical studies

Reutilization of precursor following axonal transport of [3H]proline-labeled protein

In further studies on axonally transported protein in the goldfish visual system, the turnover of rapidly transported [3H]proline-labeled protein was examined. It was found that: (1) a fraction of the rapidly transported protein has a relatively short half-life; (2) [3H]proline released following proteolysis of transported protein is efficiently reutilized for tectal protein synthesis, as inferred from an increased labeling of nuclear protein in the contralateral tectum (COT) relative to that in the ipsilateral tectum (IOT); (3) a small amount of [3H]proline arrives in the COT by axonal flow of the free amino acid; and (4) [3H]leucine and [3H]asparagine are less efficiently reutilized than [3H]proline.These findings may relate to the phenomenon of transneuronal transfer of radio-activity which has been observed with [3H]proline as precursor. The extensive reutilization of [3H]proline may account for part or all of the labeling at secondary synaptic sites. The results suggest that asparagine may be highly suitable for radioautographic identification of primary neuronal fields.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22980/1/0000547.pd

Current status and future perspective of flattening filter free photon beams

Purpose: Flattening filters (FFs) have been considered as an integral part of the treatment head of a medical accelerator for more than 50 years. The reasons for the longstanding use are, however, historical ones. Advanced treatment techniques, such as stereotactic radiotherapy or intensity modulated radiotherapy have stimulated the interest in operating linear accelerators in a flattening filter free (FFF) mode. The current manuscript reviews treatment head physics of FFF beams, describes their characteristics and the resulting potential advantages in their medical use, and closes with an outlook. Methods: A number of dosimetric benefits have been determined for FFF beams, which range from increased dose rate and dose per pulse to favorable output ratio in-air variation with field size, reduced energy variation across the beam, and reduced leakage and out-of-field dose, respectively. Finally, the softer photon spectrum of unflattened beams has implications on imaging strategies and radiation protection. Results: The dosimetric characteristics of FFF beams have an effect on treatment delivery, patient comfort, dose calculation accuracy, beam matching, absorbed dose determination, treatment planning, machine specific quality assurance, imaging, and radiation protection. When considering conventional C-arm linacs in a FFF mode, more studies are needed to specify and quantify the clinical advantages, especially with respect to treatment plan quality and quality assurance. Conclusions: New treatment units are already on the market that operate without a FF or can be operated in a dedicated clinical FFF mode. Due to the convincing arguments of removing the FF, it is expected that more vendors will offer dedicated treatment units for advanced photon beam therapy in the near future. Several aspects related to standardization, dosimetry, treatment planning, and optimization need to be addressed in more detail in order to facilitate the clinical implementation of unflattened beams. (C) 2011 American Association of Physicists in Medicine. [DOI: 10.1118/1.3554643