Ex vivo radiation sensitivity assessment for individual head and neck cancer patients using deep learning-based automated nuclei and DNA damage foci detection.

Introduction: Tumor biopsy tissue response to ex vivo irradiation is potentially an interesting biomarker for in vivo tumor response, therefore, for treatment personalization. Tumor response ex vivo can be characterized by DNA damage response, expressed by the large-scale presence of DNA damage foci in tumor nuclei. Currently, characterizing tumor nuclei and DNA damage foci is a manual process that takes hours per patient and is subjective to inter-observer variability, which is not feasible in for clinical decision making. Therefore, our goal was to develop a method to automatically segment nuclei and DNA damage foci in tumor tissue samples treated with radiation ex vivo to characterize the DNA damage response, as potential biomarker for in vivo radio-sensitivity. Methods: Oral cavity tumor tissue of 21 patients was irradiated ex vivo (5 or 0 Gy), fixated 2 h post-radiation, and used to develop our method for automated nuclei and 53BP1 foci segmentation. The segmentation model used both deep learning and conventional image-analysis techniques. The training (22 %), validation (22 %), and test set (56 %) consisted of thousands of manually segmented nuclei and foci. The segmentations and number of foci per nucleus in the test set were compared to their ground truths. Results: The automatic nuclei and foci segmentations were highly accurate (Dice = 0.901 and Dice = 0.749, respectively). An excellent correlation (R2 = 0.802) was observed for the foci per nucleus that outperformed reported inter-observation variation. The analysis took âˆ¼ 8 s per image. Conclusion: This model can replace manual foci analysis for ex vivo irradiation of head-and-neck squamous cell carcinoma tissue, reduces the image-analysis time from hours to minutes, avoids the problem of inter-observer variability, enables assessment of multiple images or conditions, and provides additional information about the foci size. Thereby, it allows for reliable and rapid ex vivo radio-sensitivity assessment, as potential biomarker for response in vivo and treatment personalization.

Iodide-induced sialadenitis following percutaneous coronary intervention: A case report.

Iodide-induced sialadenitis is a rapid, painless enlargement of salivary glands following administration of iodine-based contrast agents. It has been reported numerous times in the literature; however, the pathogenesis remains unclear. This case report demonstrates how this may present following a coronary angiogram.

Stability and Resiliency of Biological Control of the Twospotted Spider Mite (Acari: Tetranychidae) in Hop.

The twospotted spider mite (Tetranychus urticae Koch) is a common pest in agricultural and ornamental crops. This pest can be controlled by resident predatory arthropods in certain situations. This research quantified the stability and resiliency of established conservation biological control of the twospotted spider mite in hop over a 5-yr period associated with nitrogen fertilization rate and use of a broad-spectrum insecticide. Biological control generally was stable and resilient over a sixfold range of nitrogen fertilization rates, and in only 1 of 5 yr did elevated nitrogen rates significantly affect populations of spider mites. In contrast, one application of the insecticide bifenthrin was associated with disruption of biological control and a severe outbreak of spider mites. The complex of natural enemies suppressed the outbreak during the same year in which bifenthrin was applied, but only after populations of spider mites exceeded levels associated with economic damage. However, in the following year the system returned to an equilibrium state where spider mites were suppressed below economically damaging levels. Therefore, conservation biological control in hop appears stable and robust to factors such as nitrogen fertilization that increase reproductive rates of spider mites but may be sensitive to factors such as nonselective insecticides that are lethal to natural enemies. Conservation biological control can be considered resilient to a single use of a nonselective insecticide in the year following the application, but not within the year of application.

Genome Sequencing and Transcriptome Analysis of the Hop Downy Mildew Pathogen Pseudoperonospora humuli Reveal Species-Specific Genes for Molecular Detection.

Pseudoperonospora humuli is an obligate oomycete pathogen of hop (Humulus lupulus) that causes downy mildew, an important disease in most production regions in the Northern Hemisphere. The pathogen can cause a systemic infection in hop, overwinter in the root system, and infect propagation material. Substantial yield loss may occur owing to P. humuli infection of strobiles (seed cones), shoots, and cone-bearing branches. Fungicide application and cultural practices are the primary methods to manage hop downy mildew. However, effective, sustainable, and cost-effective management of downy mildew can be improved by developing early detection systems to inform on disease risk and timely fungicide application. However, no species-specific diagnostic assays or genomic resources are available for P. humuli. The genome of the P. humuli OR502AA isolate was partially sequenced using Illumina technology and assembled with ABySS. The assembly had a minimum scaffold length of 500 bp and an N50 (median scaffold length of the assembled genome) of 19.2 kbp. A total number of 18,656 genes were identified using MAKER standard gene predictions. Additionally, transcriptome assemblies were generated using RNA-seq and Trinity for seven additional P. humuli isolates. Bioinformatics analyses of next generation sequencing reads of P. humuli and P. cubensis (a closely related sister species) identified 242 candidate species-specific P. humuli genes that could be used as diagnostic molecular markers. These candidate genes were validated using polymerase chain reaction against a diverse collection of isolates from P. humuli, P. cubensis, and other oomycetes. Overall, four diagnostic markers were found to be uniquely present in P. humuli. These candidate markers identified through comparative genomics can be used for pathogen diagnostics in propagation material, such as rhizomes and vegetative cuttings, or adapted for biosurveillance of airborne sporangia, an important source of inoculum in hop downy mildew epidemics.

Influence of Nitrogen Fertilizer Rate on Hop Looper.

Hop looper, Hypena humuli Harris, can cause substantial defoliation and crop damage by feeding on hop leaves and cones. A 4-yr field study conducted in western Oregon evaluated the abundance of hop looper larvae and associated defoliation of leaves on plants fertilized with nitrogen rates ranging from 44.8 to 269 kg/ha. There was annual variation in abundance of hop looper and defoliation, with a tendency for increasing nitrogen rate to increase both abundance of hop looper and defoliation. A mixed model analysis with data combined from 2014 to 2017 found that abundance of hop looper was linearly related to nitrogen fertilizer rate, with a 2.5 increase in hop looper-days per kilogram of nitrogen fertilizer applied. Similarly, based on data from 2015 to 2017, defoliation associated with hop looper increased 0.031 percent with each kilogram of nitrogen fertilizer applied. Therefore, avoiding unduly high rates of nitrogen fertilizer may reduce the abundance and defoliation caused by hop looper. Further studies are needed to understand the mechanisms associated with nitrogen stimulation of hop looper.

Environmental Electrokinetics for a sustainable subsurface.

Soil and groundwater are key components in the sustainable management of the subsurface environment. Source contamination is one of its main threats and is commonly addressed using established remediation techniques such as in-situ chemical oxidation (ISCO), in-situ chemical reduction (ISCR; most notably using zero-valent iron [ZVI]), enhanced in-situ bioremediation (EISB), phytoremediation, soil-washing, pump-and-treat, soil vapour extraction (SVE), thermal treatment, and excavation and disposal. Decades of field applications have shown that these techniques can successfully treat or control contaminants in higher permeability subsurface materials such as sands, but achieve only limited success at sites where low permeability soils, such as silts and clays, prevail. Electrokinetics (EK), a soil remediation technique mostly recognized in in-situ treatment of low permeability soils, has, for the last decade, been combined with more conventional techniques and can significantly enhance the performance of several of these remediation technologies, including ISCO, ISCR, EISB and phytoremediation. Herein, we discuss the use of emerging EK techniques in tandem with conventional remediation techniques, to achieve improved remediation performance. Furthermore, we highlight new EK applications that may come to play a role in the sustainable treatment of the contaminated subsurface.

Using Next-Generation Sequencing to Develop Molecular Diagnostics for Pseudoperonospora cubensis, the Cucurbit Downy Mildew Pathogen.

Advances in next-generation sequencing (NGS) allow for rapid development of genomics resources needed to generate molecular diagnostics assays for infectious agents. NGS approaches are particularly helpful for organisms that cannot be cultured, such as the downy mildew pathogens, a group of biotrophic obligate oomycetes that infect crops of economic importance. Unlike most downy mildew pathogens that are highly host-specific, Pseudoperonospora cubensis causes disease on a broad range of crops belonging to the family Cucurbitaceae. In this study, we identified candidate diagnostic markers for P. cubensis by comparing NGS data from a diverse panel of P. cubensis and P. humuli isolates, two very closely related oomycete species. P. cubensis isolates from diverse hosts and geographical regions in the United States were selected for sequencing to ensure that candidates were conserved in P. cubensis isolates infecting different cucurbit hosts. Genomic regions unique to and conserved in P. cubensis isolates were identified through bioinformatics. These candidate regions were then validated using PCR against a larger collection of isolates from P. cubensis, P. humuli, and other oomycetes. Overall seven diagnostic markers were found to be specific to P. cubensis. These markers could be used for pathogen diagnostics on infected tissue, or adapted for monitoring airborne inoculum with real-time PCR and spore traps.

Targeted inhibition of metastatic melanoma through interference with Pin1-FOXM1 signaling.

Melanoma is the most lethal form of skin cancer and successful treatment of metastatic melanoma remains challenging. BRAF/MEK inhibitors only show a temporary benefit due to rapid occurrence of resistance, whereas immunotherapy is mainly effective in selected subsets of patients. Thus, there is a need to identify new targets to improve treatment of metastatic melanoma. To this extent, we searched for markers that are elevated in melanoma and are under regulation of potentially druggable enzymes. Here, we show that the pro-proliferative transcription factor FOXM1 is elevated and activated in malignant melanoma. FOXM1 activity correlated with expression of the enzyme Pin1, which we found to be indicative of a poor prognosis. In functional experiments, Pin1 proved to be a main regulator of FOXM1 activity through MEK-dependent physical regulation during the cell cycle. The Pin1-FOXM1 interaction was enhanced by BRAF(V600E), the driver oncogene in the majority of melanomas, and in extrapolation of the correlation data, interference with\ Pin1 in BRAF(V600E)-driven metastatic melanoma cells impaired both FOXM1 activity and cell survival. Importantly, cell-permeable Pin1-FOXM1-blocking peptides repressed the proliferation of melanoma cells in freshly isolated human metastatic melanoma ex vivo and in three-dimensional-cultured patient-derived melanoids. When combined with the BRAF(V600E)-inhibitor PLX4032 a robust repression in melanoid viability was obtained, establishing preclinical value of patient-derived melanoids for prognostic use of drug sensitivity and further underscoring the beneficial effect of Pin1-FOXM1 inhibitory peptides as anti-melanoma drugs. These proof-of-concept results provide a starting point for development of therapeutic Pin1-FOXM1 inhibitors to target metastatic melanoma.

The association between green space and depressive symptoms in pregnant women: moderating roles of socioeconomic status and physical activity.

BACKGROUND: The current study explored the association between green space and depression in a deprived, multiethnic sample of pregnant women, and examined moderating and mediating variables. METHOD: 7547 women recruited to the 'Born in Bradford' cohort completed a questionnaire during pregnancy. A binary measure of depressive symptoms was calculated using a validated survey. Two green space measures were used: quintiles of residential greenness calculated using the normalised difference vegetation index for three neighbourhood sizes (100, 300 and 500 m buffer zones around participant addresses); access to major green spaces estimated as straight line distance between participant address and nearest green space (>0.5 hectares). Logistic regression analyses examined relationships between green space and depressive symptoms, controlling for ethnicity, demographics, socioeconomic status (SES) and health behaviours. Multiplicative interactions explored variations by ethnic group, SES or activity levels. Mediation analysis assessed indirect effects via physical activity. RESULTS: Pregnant women in the greener quintiles were 18-23% less likely to report depressive symptoms than those in the least green quintile (for within 100 m of green space buffer zone). The green space-depressive symptoms association was significant for women with lower education or who were active. Physical activity partially mediated the association of green space, but explained only a small portion of the direct effect. CONCLUSIONS: Higher residential greenness was associated with a reduced likelihood of depressive symptoms. Associations may be stronger for more disadvantaged groups and for those who are already physically active. Improving green space is a promising intervention to reduce risk of depression in disadvantaged groups.

Development of biological control of Tetranychus urticae (Acari: Tetranychidae) and Phorodon humuli (Hemiptera: Aphididae) in Oregon hop yards.

The temporal development of biological control of arthropod pests in perennial cropping systems is largely unreported. In this study, the development of biological control of twospotted spider mite, Tetranychus urticae Koch, and hop aphid, Phorodon humuli (Schrank), in a new planting of hop in Oregon is described over a period of 9 yr (2005-2013). Both the abundance and diversity of natural enemies increased over time. Known predators of hop aphid (Coccinellidae and Anthocoridae) were present in all years; however, stable biological control of hop aphid was not achieved in most years and aphicides were required to suppress populations at commercially acceptable levels in 5 of 9 yr. Populations of aphidophagous coccinellids developed synchronously with hop aphid populations, and temporal correlations indicated these are the primary predatory insect associated with hop aphid regulation. However, sampling methods did not assess levels of aphid parasitoids and hyperparasitoids and their contribution to biological control was unquantified. Spider mite biological control was associated primarily with predatory mites (Phytoseiidae) and Stethorus spp. (Coccinellidae). The magnitude of temporal correlations of abundance of these predators with spider mites was found to be greatest on the same sampling dates and at lags of 7-14 d. Stable biological control of spider mites occurred after four field seasons, suppressing spider mites to levels similar to those commonly achieved with chemical control. A survey of 11 commercial hop yards in Oregon documented pest and natural enemy densities under commercial management practices over a period of 4 yr (2008-2011). Natural enemy abundance in commercial hop yards was similar to that of a 2- to 3-yr-old hop yard with limited disturbance. Whereas total reliance on biological control for hop aphid is unlikely to be successful, there appears to be unrealized potential for biological control of spider mites in commercial production. Dynamic action thresholds that consider the value of natural enemies are needed for both pests.

Suppression of hop looper (Lepidoptera: Noctuidae) by the fungicide pyraclostrobin.

The hop looper, Hypena humuli Harris, is a reemergent pest of hop that often requires treatment to mitigate crop damage. In 4 yr of field trials, plots treated with fungicides were observed to sustain less hop looper defoliation compared with nontreated plots. Further investigation revealed that abundance of hop looper and associated defoliation were reduced when the fungicide pyraclostrobin was applied in late July to early August. Two other fungicides possessing active ingredients in the same chemical family (quinone outside inhibitor) did not reduce abundance of hop looper or its defoliation. Pyraclostrobin is efficacious against powdery mildew diseases, and the application timing evaluated in these studies corresponds with a period of juvenile susceptibility of hop cones to the disease. Use of fungicides containing pyraclostrobin at this time may have the ancillary benefit of reducing hop looper damage, potentially obviating the need for broad-spectrum insecticides later in the season. Follow-up studies are warranted to determine whether pyraclostrobin may inhibit other lepidopteran species.

Powdery Mildew Outbreaks caused by Podosphaera macularis on Hop Cultivars Possessing the Resistance Gene R6 in the Pacific Northwestern United States.

Resistant cultivars of hop (Humulus lupulus) have been grown, with the aim of helping to manage powdery mildew in the Pacific Northwest since the first report of the disease in the field in 1997 (4). A major objective of many breeding programs is development of resistance to powdery mildew, and this has generally been achieved by single resistance genes (qualitative resistance). One such gene, R6 (3), has been utilized extensively in new cultivars and has prevented epidemics of the disease in those cultivars across the Pacific Northwestern United States for approximately 15 years. In 2011, a grower in Washington State reported outbreaks of powdery mildew on cv. Apollo, which is thought to possess powdery mildew resistance derived from R6. Fungicides and cultural control measures were applied, and the grower reported no substantial crop damage from the disease. During the winter of 2012, the same grower planted rhizomes of cv. Apollo in a greenhouse in the Yakima Valley of Washington State and later found the plants to be affected by powdery mildew. Affected leaves from plants of cvs. Apollo, Newport, and Nugget (all reported [3] or assumed to possess R6 based on pedigree) grown in the same greenhouse were later provided to the authors. Conidia obtained from each affected plants were transferred to plants of the highly susceptible cv. Symphony, which is not known to contain any resistance genes. After 10 to 14 days of incubation, resultant conidia from each cultivar above (total of three isolates) were transferred to greenhouse grown plants of cvs. Nugget and Symphony and incubated at 18°C. Within 7 days, all three isolates produced powdery mildew colonies characteristic of P. macularis (2) on both cultivars. Cleistothecia did not develop in any colonies. In addition, Nugget and Symphony plants were inoculated with a field population of P. macularis originating from cultivars lacking R6 in Oregon. These inoculations on Nugget did not develop powdery mildew whereas Symphony plants did. Non-inoculated controls remained free of powdery mildew. Results were identical in two additional experiments. The sequence of the mating type idiomorph, MAT1-1, was obtained to confirm identity of the pathogen as P. macularis as described previously (1). The sequences were identical among the three isolates obtained from the greenhouse in Washington and isolates of P. macularis obtained previously from Oregon and Washington. MAT1-2 idiomorph was not detected in the isolates collected. While R6-virulent strains have been detected previously in race characterization experiments, these strains have not caused widespread epidemics of powdery mildew. The increasing prevalence of virulent strains of P. macularis and outbreaks of powdery mildew on formerly resistant cultivars necessitates changes in breeding strategies and disease management efforts to minimize damage resulting from the disease. The distribution of virulent strains of the pathogen and susceptibility of formerly resistance cultivars to powdery mildew are currently under investigation. References: (1) B. Asalfet et al. Phytopathology 103:717, 2013. (2) R. Bélanger et al. The Powdery Mildews: a Comprehensive Treatise. APS Press, St. Paul, MN, 2002. (3) P. Darby. Brew Hist. 121:94, 2005. (4) C. Ocamb et al. Plant Dis. 83:1072, 1999.

From DNA damage to chromosome aberrations: joining the break.

Despite many years of experimental studies on radiation-induced chromosomal aberrations, and the recent progress in elucidating the molecular mechanisms of the DNA damage response, the link between DNA double-strand break repair and its expression as microscopically visible chromosomal rearrangements remains, in many ways, obscure. Some long standing controversies have partially been resolved to the satisfaction of most investigators, including the linearity of the dose-response for DNA double-strand break induction, the necessity of pairwise interaction of radiogenic damaged sites in the formation of exchange aberrations, and the importance of proximity between lesions in misrejoining. However, the contribution of different molecular DNA repair mechanisms (e.g., alternative end-joining pathways) and their impact on the kinetics of aberration formation is still unclear, as is the definition of "complex" radiogenic damaged sites - in either the chemical or spatial sense - which ostensibly lead to chromosome rearrangements. These topics have been recently debated by molecular biologists and cytogeneticists, whose opinions are summarized in this paper.

Population density and phenology of Tetranychus urticae (Acari: Tetranychidae) in hop is linked to the timing of sulfur applications.

The twospotted spider mite, Tetranychus urticae Koch, is a worldwide pest of numerous agronomic and horticultural plants. Sulfur fungicides are known to induce outbreaks of this pest on several crops, although mechanisms associated with sulfur-induced mite outbreaks are largely unknown. Studies were conducted during 2007-2009 in Oregon and Washington hop yards to evaluate the effect of timing of sulfur applications on T. urticae and key predators. In both regions, applications of sulfur made relatively late in the growing season (mid-June to mid-July) were associated with the greatest exacerbation of spider mite outbreaks, particularly in the upper canopy of the crop. The severity of mite outbreaks was closely associated with sulfur applications made during a relatively narrow time period coincident with the early exponential phase of spider mite increase and rapid host growth. A nonlinear model relating mean cumulative mite days during the time of sulfur sprays to the percent increase in total cumulative mite days (standardized to a nontreated plot) explained 58% of the variability observed in increased spider mite severity related to sulfur spray timing. Spatial patterns of spider mites in the Oregon plots indicated similar dispersal of motile stages of spider mites among leaves treated with sulfur versus nontreated leaves; however, in two of three years, eggs were less aggregated on leaves of sulfur-treated plants, pointing to enhanced dispersal. Apart from one experiment in Washington, relatively few predatory mites were observed during the course of these studies, and sulfur-induced mite outbreaks generally occurred irrespective of predatory mite abundance. Collectively, these studies indicate sulfur induces mite outbreaks through direct or indirect effects on T. urticae, mostly independent of predatory mite abundance or toxicity to these predators. Avoidance of exacerbation of spider mite outbreaks by sulfur sprays was achieved by carefully timing applications to periods of low spider mite abundance and slower host development, which is generally early to mid-spring for hop.

Sclerotinia Wilt of Hop (Humulus lupulus) Caused by Sclerotinia sclerotiorum in the Pacific Northwest United States.

In June 2009, wilted hop bines were observed in a yard in Marion County, OR. The wilt was associated with a stem rot that occurred ~1 m from the ground near the point where bines are tied together for horticultural purposes. Samples of affected stems were submitted to the Oregon State University Plant Clinic. White hyphae and large, black sclerotia were present on the stems, with a clear delineation between healthy and diseased tissue. The pathogen was identified as Sclerotinia sclerotiorum based on morphological characters. In June 2011, bine wilting was observed on the same farm but in a different hop yard (cv. Nugget) ~10 km from the 2009 occurrence. Affected plants had upward curled leaves with necrotic margins or wilted bines that were severed at the soil line. Wilted bines tended to have smaller diameters than bines with foliar symptoms only. Of 100 plants examined, 75% displayed some foliar symptoms and 66% had at least one bine that was wilted. Yield loss was estimated at 10 to 20% due to bine wilting before cone development. Unlike the 2009 occurrence, wilted bines did not display aerial signs of S. sclerotiorum. Rather, water-soaked lesions covered in white, cottony mycelium were apparent on affected stems 2.5 to 5 cm below the soil surface, some bearing large, irregularly shaped sclerotia. Isolations made onto potato dextrose agar yielded isolates with rapid growth rates and morphological characters consistent with S. sclerotiorum (1). DNA was extracted (2) and pathogen identity was confirmed by PCR amplification and sequencing of the internal transcribed spacer regions from isolates SS001 and SS002 as described before (4). The amplicons were sequenced bidirectionally and consensus sequences were 100% similar to S. sclerotiorum (GenBank No. AAGT01000678.1). Two nucleotide polymorphisms were present that differentiated the sequences from those of 12 S. trifoliorum accessions in GenBank that could be aligned (2). Greenhouse assays utilizing a toothpick inoculation procedure (3) were conducted to fulfill Koch's postulates. Stems of five 4-week-old hop plants of cv. Agate were pierced with a toothpick colonized with S. sclerotiorum. Five control plants were similarly inoculated with toothpicks without the fungus. Inoculated plants developed symptoms similar to those observed in the field within 11 days; four of five plants inoculated with isolate SS001 and two of five plants inoculated with isolate SS002 completely wilted. S. sclerotiorum was reisolated from all inoculated plants but not the control plants. To our knowledge, this is the first report of Sclerotinia wilt on hop in Oregon or the Pacific Northwest (1), where nearly all commercial hop production occurs in the United States. The disease appears to be localized to a limited number of yards, although given the widespread distribution and host range of S. sclerotiorum, it is plausible that the disease may occur in other yards. Recurrent outbreaks and spread of the disease among yards on the affected farm suggests that Sclerotinia wilt has the potential to become a perennial problem on hop and efforts to limit the introduction of S. sclerotiorum into other yards are warranted. References: (1) D. H. Gent. Page 32 in: Compendium of Hop Diseases and Pests. The American Phytopathological Society, St. Paul, MN, 2009. (2) E. N. Njambere et al. Plant Dis. 92:917, 2008. (3) M. L. Putnam. Plant Pathol. 53:252, 2004. (4) T. J. White et al. PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990.

Sensitivity of Disease Management Decision Aids to Temperature Input Errors Associated with Sampling Interval and Out-of-Canopy Sensor Placement.

Many plant disease epidemic models, and the disease management decision aids developed from them, are created based on temperature or other weather conditions measured in or above the crop canopy at intervals of 15 or 30 min. Disease management decision aids, however, commonly are implemented based on hourly weather measurements made from sensors sited at a standard placement of 1.5 m above the ground or are estimated from off-site weather measurements. We investigated temperature measurement errors introduced when sampling interval was increased from 15 to 60 min, and when actual in-canopy conditions were represented by temperature measurements collected by standard-placement sensors (1.5 m above the ground, outside the canopy) in each of three crops (grass seed, grape, and hops) and assessed the impact of these errors on outcomes of decision aids for grass stem rust as well as grape and hops powdery mildews. Decreasing time resolution from 15 to 60 min resulted in statistically significant underestimates of daily maximum temperatures and overestimates of daily minimum temperatures that averaged 0.2 to 0.4°C. Sensor location (in-canopy versus standard-placement) also had a statistically significant effect on measured temperature, and this effect was significantly less in grape or hops than in the grass seed crop. Effects of these temperature errors on performance of disease management decision aids were affected by magnitude of the errors as well as the type of decision aid. The grape and hops powdery mildew decision aids used rule-based indices, and the relatively small (±0.8°C) differences in temperature observed between in-canopy and standard placement sensors in these crops resulted in differences in rule outcomes when actual in-canopy temperatures were near a threshold for declaring that a rule had been met. However, there were only minor differences in the management decision (i.e., fungicide application interval). The decision aid for grass stem rust was a simulation model, for which temperature recording errors associated with location of the weather station resulted in incremental (not threshold) effects on the model of pathogen growth and plant infection probability. Simple algorithms were devised to correct the recorded temperatures or the computed infection probability to produce outcomes similar to those resulting from in-canopy temperature measurements. This study illustrates an example of evaluating (and, if necessary, correcting) temperature measurement errors from weather station sensors not located within the crop canopy, and provides an estimate of uncertainty in temperature measurements associated with location and sampling interval of weather station sensors.

Evaluation of airborne methyl salicylate for improved conservation biological control of two-spotted spider mite and hop aphid in Oregon hop yards.

The use of synthetic herbivore-induced plant volatiles (HIPV) to attract natural enemies has received interest as a tool to enhance conservation biological control (CBC). Methyl salicylate (MeSA) is a HIPV that is attractive to several key predators of two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), and hop aphid, Phorodon humuli (Schrank) (Homoptera: Aphididae). A 2-year study was conducted to evaluate the recommended commercial use of MeSA in hop yards in Oregon. Slow-release MeSA dispensers were stapled to supporting poles in 0.5 ha plots and these plots were compared to a paired non-treated plot on each of three farms in 2008 and 2009. Across both years, there was a trend for reduced (range 40-91%) mean seasonal numbers of T. urticae in five of the six MeSA-baited plots. Stethorus spp., key spider mite predators, tended to be more numerous in MeSA-baited plots compared to control plots on a given farm. Mean seasonal densities of hop aphid and other natural enemies (e.g., Orius spp. and Anystis spp.) were similar between MeSA-treated and control plots. Variability among farms in suppression of two-spotted spider mites and attraction of Stethorus spp. suggests that the use of MeSA to enhance CBC of spider mites in commercial hop yards may be influenced by site-specific factors related to the agroecology of individual farms or seasonal effects that require further investigation. The current study also suggests that CBC of hop aphid with MeSA in this environment may be unsatisfactory.

Comments regarding the binary power law for heterogeneity of disease incidence.

The binary power law (BPL) has been successfully used to characterize heterogeneity (overdispersion or small-scale aggregation) of disease incidence for many plant pathosystems. With the BPL, the log of the observed variance is a linear function of the log of the theoretical variance for a binomial distribution over the range of incidence values, and the estimated scale (?) and slope (b) parameters provide information on the characteristics of aggregation. When b = 1, the interpretation is that the degree of aggregation remains constant over the range of incidence values observed; otherwise, aggregation is variable. In two articles published in this journal in 2009, Gosme and Lucas used their stochastic simulation model, Cascade, to show a multiphasic (split-line) relationship of the variances, with straight-line (linear) relationships on a log-log scale within each phase. In particular, they showed a strong break point in the lines at very low incidence, with b considerably >1 in the first line segment (corresponding to a range of incidence values usually not observed in the field), and b being ?1 in the next segment (corresponding to the range of incidence values usually observed). We evaluated their findings by utilizing a general spatially explicit stochastic simulator developed by Xu and Ridout in 1998, with a wide range of median dispersal distances for the contact distribution and number of plants in the sampling units (quadrats), and through an assessment of published BPL results. The simulation results showed that the split-line phenomenon can occur, with a break point at incidence values of ?0.01; however, the split is most obvious for short median dispersal distances and large quadrat sizes. However, values of b in the second phase were almost always >1, and only approached 1 with extremely short median dispersal distances and small quadrat sizes. An appraisal of published results showed no evidence of multiple phases (although the minimum incidence may generally be too high to observe the break), and estimates of b were almost always >1. Thus, it appears that the results from the Cascade simulation model represent a special epidemiological case, corresponding primarily to a roughly nearest-neighbor population-dynamic process. Implications of a multiphasic BPL property may be important and are discussed.

Artemis splice defects cause atypical SCID and can be restored in vitro by an antisense oligonucleotide.

Artemis deficiency is known to result in classical T-B- severe combined immunodeficiency (SCID) in case of Artemis null mutations, or Omenn's syndrome in case of hypomorphic mutations in the Artemis gene. We describe two unrelated patients with a relatively mild clinical T-B- SCID phenotype, caused by different homozygous Artemis splice-site mutations. The splice-site mutations concern either dysfunction of a 5' splice-site or an intronic point mutation creating a novel 3' splice-site, resulting in mutated Artemis protein with residual activity or low levels of wild type (WT) Artemis transcripts. During the first 10 years of life, the patients suffered from recurrent infections necessitating antibiotic prophylaxis and intravenous immunoglobulins. Both mutations resulted in increased ionizing radiation sensitivity and insufficient variable, diversity and joining (V(D)J) recombination, causing B-lymphopenia and exhaustion of the naive T-cell compartment. The patient with the novel 3' splice-site had progressive granulomatous skin lesions, which disappeared after stem cell transplantation (SCT). We showed that an alternative approach to SCT can, in principle, be used in this case; an antisense oligonucleotide (AON) covering the intronic mutation restored WT Artemis transcript levels and non-homologous end-joining pathway activity in the patient fibroblasts.

Decision aids for multiple-decision disease management as affected by weather input errors.

Many disease management decision support systems (DSSs) rely, exclusively or in part, on weather inputs to calculate an indicator for disease hazard. Error in the weather inputs, typically due to forecasting, interpolation, or estimation from off-site sources, may affect model calculations and management decision recommendations. The extent to which errors in weather inputs affect the quality of the final management outcome depends on a number of aspects of the disease management context, including whether management consists of a single dichotomous decision, or of a multi-decision process extending over the cropping season(s). Decision aids for multi-decision disease management typically are based on simple or complex algorithms of weather data which may be accumulated over several days or weeks. It is difficult to quantify accuracy of multi-decision DSSs due to temporally overlapping disease events, existence of more than one solution to optimizing the outcome, opportunities to take later recourse to modify earlier decisions, and the ongoing, complex decision process in which the DSS is only one component. One approach to assessing importance of weather input errors is to conduct an error analysis in which the DSS outcome from high-quality weather data is compared with that from weather data with various levels of bias and/or variance from the original data. We illustrate this analytical approach for two types of DSS, an infection risk index for hop powdery mildew and a simulation model for grass stem rust. Further exploration of analysis methods is needed to address problems associated with assessing uncertainty in multi-decision DSSs.