Dynamic classification using case-specific training cohorts outperforms static gene expression signatures in breast cancer

The molecular diversity of breast cancer makes it impossible to identify prognostic markers that are applicable to all breast cancers. To overcome limitations of previous multigene prognostic classifiers, we propose a new dynamic predictor: instead of using a single universal training cohort and an identical list of informative genes to predict the prognosis of new cases, a case-specific predictor is developed for each test case. Gene expression data from 3,534 breast cancers with clinical annotation including relapse-free survival is analyzed. For each test case, we select a case-specific training subset including only molecularly similar cases and a case-specific predictor is generated. This method yields different training sets and different predictors for each new patient. The model performance was assessed in leave-one-out validation and also in 325 independent cases. Prognostic discrimination was high for all cases (n = 3,534, HR = 3.68, p = 1.67 E-56). The dynamic predictor showed higher overall accuracy (0.68) than genomic surrogates for Oncotype DX (0.64), Genomic Grade Index (0.61) or MammaPrint (0.47). The dynamic predictor was also effective in triple-negative cancers (n = 427, HR = 3.08, p = 0.0093) where the above classifiers all failed. Validation in independent patients yielded similar classification power (HR = 3.57). The dynamic classifier is available online at http://www.recurrenceonline.com/?q=Re_training. In summary, we developed a new method to make personalized prognostic prediction using case-specific training cohorts. The dynamic predictors outperform static models developed from single historical training cohorts and they also predict well in triple-negative cancers

Quality assurance in stereotactic radiosurgery/radiotherapy according to DIN 6875-1

The new DIN (' Deutsche Industrie- Norm') 6875- 1, which is currently being finalised, deals with quality assurance ( QA) criteria and tests methods for linear accelerator and Gamma Knife stereotactic radiosurgery/ radiotherapy including treatment planning, stereotactic frame and stereotactic imaging and a system test to check the whole chain of uncertainties. Our existing QA program, based on dedicated phantoms and test procedures, has been refined to fulfill the demands of this new DIN. The radiological and mechanical isocentre corresponded within 0.2 mm and the measured 50% isodose lines were in agreement with the calculated ones within less than 0.5 mm. The measured absorbed dose was within 3%. The resultant output factors measured for the 14-, 8- and 4- mm collimator helmet were 0.9870 +/- 0.0086, 0.9578 +/- 0.0057 and 0.8741 +/- 0.0202, respectively. For 170 consecutive tests, the mean geometrical accuracy was 0.48 +/- 0.23 mm. Besides QA phantoms and analysis software developed in- house, the use of commercially available tools facilitated the QA according to the DIN 6875- 1 with which our results complied. Copyright (C) 2004 S. Karger AG, Basel

Effectiveness of Prescribed Fire to Re-Establish Sagebrush Steppe Vegetation and Ecohydrologic Function on Woodland-Encroached Sagebrush Rangelands, Great Basin, USA: Part I: Vegetation, Hydrology, and Erosion Responses

Pinyon (Pinus spp.) and juniper (Juniperus spp.) woodland encroachment has imperiled a broad ecological domain of the sagebrush steppe (Artemisia spp.) ecosystem in the Great Basin Region, USA. As these conifers increase in dominance on sagebrush rangelands, understory vegetation declines and ecohydrologic function can shift from biotic (vegetation) controlled retention of soil resources to abiotic (runoff) driven loss of soil resources and long-term site degradation. Scientists, public land management agencies, and private land owners are challenged with selecting and predicting outcomes to treatment alternatives to improve ecological structure and function on these rangelands. This study is the first of a two-part study to evaluate effectiveness of prescribed fire to re-establish sagebrush steppe vegetation and improve ecohydrologic function on mid- to late-succession pinyon-and juniper-encroached sagebrush sites in the Great Basin. We used a suite of vegetation and soil measures, small-plot (0.5 m2) rainfall simulations, and overland flow experiments (9 m2) to quantify the effects of tree removal by prescribed fire on vegetation, soils, and rainsplash, sheetflow, and concentrated flow hydrologic and erosion processes at two woodlands 9-yr after burning. For untreated conditions, extensive bare interspace (87% bare ground) throughout the degraded intercanopy (69–88% bare ground) between trees at both sites promoted high runoff and sediment yield from combined rainsplash and sheetflow (~45 mm, 59–381 g m−2) and concentrated flow (371–501 L, 2343–3015 g) processes during high intensity rainfall simulation (102 mm h−1, 45 min) and overland flow experiments (15, 30, and 45 L min−1, 8 min each). Burning increased canopy cover of native perennial herbaceous vegetation by \u3e5-fold, on average, across both sites over nine growing seasons. Burning reduced low pre-fire sagebrush canopy cover (30 yr. Enhanced herbaceous cover in interspaces post-fire reduced runoff and sediment yield from high intensity rainfall simulations by \u3e2-fold at both sites. Fire-induced increases in herbaceous canopy cover (from 34% to 62%) and litter ground cover (from 15% to 36%) reduced total runoff (from 501 L to 180 L) and sediment yield (from 2343 g to 115 g) from concentrated flow experiments in the intercanopy at one site. Sparser herbaceous vegetation (49% cover) and litter cover (8%) in the intercanopy at the other, more degraded site post-fire resulted in no significant reduction of total runoff (371 L to 266 L) and sediment yield (3015 g to 1982 g) for concentrated flow experiments. Areas underneath unburned shrub and tree canopies were well covered by vegetation and ground cover and generated limited runoff and sediment. Fire impacts on vegetation, ground cover, and runoff and sediment delivery from tree and shrub plots were highly variable. Burning litter covered areas underneath trees reduced perennial herbaceous vegetation and increased invasibility to the fire-prone annual cheatgrass (Bromus tectorum L.). Cheatgrass cover increased fro

Effectiveness of Prescribed Fire to Re-Establish Sagebrush Steppe Vegetation and Ecohydrologic Function on Woodland-Encroached Sagebrush Reangelands, Great Basin, USA: Part II: Runoff and Sediment Transport at the Patch Scale

Woody species encroachment into herbaceous and shrub-dominated vegetations is a concern in many rangeland ecosystems of the world. Arrival of woody species into affected rangelands leads to changes in the spatial structure of vegetation and alterations of biophysical processes. In the western USA, encroachment of pinyon (Pinus spp.) and juniper (Juniperus spp.) tree species into sagebrush steppes poses a threat to the proper ecohydrological functioning of these ecosystems. Prescribed fire has been proposed and used as one rangeland improvement practice to restore sagebrush steppe from pinyon-juniper encroachment. Short-term effects of burning on the ecohydrologic response of these systems have been well documented and often include a period of increased hydrologic and erosion vulnerability immediately after burning. Long-term ecohydrologic response of sagebrush steppe ecosystems to fire is poorly understood due to lack of cross-scale studies on treated sites. The aim of this study is to evaluate long-term vegetation, hydrologic, and erosion responses at two pinyon-juniper-encroached sagebrush sites 9 years after prescribed fire was applied as a restoration treatment. Thirty-six rainfall simulation experiments on 6 m × 2 m plots were conducted for 45 min under two conditions: a dry run (70 mm h−1; dry antecedent soils) and a wet run (111 mm h−1; wet antecedent soils). Runoff and erosion responses were compared between burned and unburned plots. Overall, increases in herbaceous cover in the shrub-interspace areas (intercanopy area between trees) at both sites 9 years post-burn resulted in runoff- and erosion-reduction benefits, especially under the wet runs. While the initially more degraded site characterized by 80% bare ground pre-burn, registered a higher overall increase (40% increase) in canopy cover, greater post-fire reductions in runoff and erosion were observed at the less degraded site (57% bare ground pre-burn). Runoff and erosion for the wet runs decreased respectively by 6.5-fold and 76-fold at the latter site on the burned plots relative to control plots, whereas these decreases were more muted at the more degraded site (2.5 and 3-fold respectively). Significant fragmentation of flow paths observed at the more-degraded site 9 years post-fire, suggests a decreased hydrologic connectivity as a mechanism of runoff and erosion reduction during post-fire recovery

Vegetation, Hydrologic, and Erosion Responses of Sagebrush Steppe 9 Yr Following Mechanical Tree Removal

Land managers across the western United States are faced with selecting and applying tree-removal treatments on pinyon (Pinus spp.) and juniper (Juniperus spp.) woodland-encroached sagebrush (Artemisia spp.) rangelands, but current understanding of long-term vegetation and hydrological responses of sagebrush sites to tree removal is inadequate for guiding management. This study applied a suite of vegetation and soil measures (0.5 − 990 m2), small-plot rainfall simulations (0.5 m2), and overland flow experiments (9 m2) to quantify the effects of mechanical tree removal (tree cutting and mastication) on vegetation, runoff, and erosion at two mid- to late-succession woodland-encroached sagebrush sites in the Great Basin, United States, 9 yr after treatment. Low amounts of hillslope-scale shrub (3 − 15%) and grass (7 − 12%) canopy cover and extensive intercanopy (area between tree canopies) bare ground (69 − 88% bare, 75% of area) in untreated areas at both sites facilitated high levels of runoff and sediment from high-intensity (102 mm • h− 1, 45 min) rainfall simulations in interspaces (~ 45 mm runoff, 59 − 381 g • m− 2 sediment) between trees and shrubs and from concentrated overland flow experiments (15, 30, and 45 L • min− 1, 8 min each) in the intercanopy (371 − 501 L runoff, 2 342 − 3 015 g sediment). Tree cutting increased hillslope-scale density of sagebrush by 5% and perennial grass cover by twofold at one site while tree cutting and mastication increased hillslope-scale sagebrush density by 36% and 16%, respectively, and perennial grass cover by threefold at a second more-degraded (initially more sparsely vegetated) site over nine growing seasons. Cover of cheatgrass (Bromus tectorum L.) was \u3c 1% at the sites pretreatment and 1 − 7% 9 yr after treatment. Bare ground remained high across both sites 9 yr after tree removal and was reduced by treatments solely at the more degraded site. Increases in hillslope-scale vegetation following tree removal had limited impact on runoff and erosion for rainfall simulations and concentrated flow experiments at both sites due to persistent high bare ground. The one exception was reduced runoff and erosion within the cut treatments for intercanopy plots with cut-downed-trees. The cut-downed-trees provided ample litter cover and tree debris at the ground surface to reduce the amount and erosive energy of concentrated overland flow. Trends in hillslope-scale vegetation responses to tree removal in this study demonstrate the effectiveness of mechanical treatments to reestablish sagebrush steppe vegetation without increasing cheatgrass for mid- to late-succession woodland-encroached sites along the warm-dry to cool-moist soil temperature − moisture threshold in the Great Basin. Our results indicate improved hydrologic function through sagebrush steppe vegetation recruitment after mechanical tree removal on mid- to late-succession woodlands can require more than 9 yr. We anticipate intercanopy runoff and erosion rates will decrease over time at both sites as shrub and grass cover continue to increase, but follow-up tree removal will be needed to prevent pinyon and juniper recolonization. The low intercanopy runoff and erosion measured underneath isolated cut-downed-trees in this study clearly demonstrate that tree debris following mechanical treatments can effectively limit microsite-scale runoff and erosion over time where tree debris settles in good contact with the soil surface

Risk Assessment of Erosion from Concentrated Flow on Rangelands Using Overland Flow Distribution and Shear Stress Partitioning

Erosion rates of overland flow on rangelands tend to be relatively low, but under certain conditions where flow is concentrated, soil loss can be significant. Therefore, a rangeland site can be highly vulnerable to soil erosion where overland flow is likely to concentrate and exert high shear stress on soil grains. This concept is commonly applied in cropland and wildland soil erosion modeling using predictions of flow effective shear stress (shear stress applied on soil grains). However, historical approaches to partition shear stress in erosion models are computationally complex and require extensive parameterization. Furthermore, most models are not capable of predicting the conditions in which concentrated flow occurs on rangelands. In this study, we investigated the rangelands conditions at which overland flow is more likely to become concentrated and developed equations for partitioning the shear stress of concentrated flow on rangelands. A logistic equation was developed to estimate the probability of overland flow to become concentrated. Total shear stress of rangeland overland flow was partitioned into components exerted on soil, vegetation, and rock cover using field experimental data. In addition, we investigated the vegetation cover limit at which the effective shear stress component is substantially reduced, limiting the erosion rate. The results from the partitioning equations show that shear stress exerted on soil grains was relatively small in sheet flow. Shear stress exerted on soil grains in concentrated flow was significantly higher when bare soil exceeded 60% of the total surface area but decreased significantly when the bare soil area was less than 25% or when the plant base cover exceeded 20%. These percentages could be used as relative measures of hydrologic recovery for disturbed rangelands or as triggers that indicate a site is crossing a threshold beyond which soil erosion might accelerate due to the high effective shear stress

Developing a Parameterization Approach for Soil Erodibility for the Rangeland Hydrology and Erosion Model (RHEM)

Soil erodibility is a key factor for estimating soil erosion using physically based models. In this study, a new parameterization approach for estimating erodibility was developed for the Rangeland Hydrology and Erosion Model (RHEM). The approach uses empirical equations that were developed by applying piecewise regression analysis to predict the differences of erodibility before and after disturbance (i.e., wildfire, prescribed fire, and tree encroachment) and across a wide range of soil textures as a function of vegetation cover and surface slope angle. The approach combines rain splash, sheet flow, and concentrated flow erodibilities into a single parameter for modeling erodibility in most cases. We evaluated the new approach for sites representing different degrees of disturbance associated with burning and tree encroachment. Our results show that the new erodibility approach in RHEM predicts erosion at the plot scale with a satisfactory range of error in all cases. The new approach extends the applications of RHEM to a greater scope of landscapes and soil texture

Concentrated Flow Erodibility for Physically Based Erosion Models: Temporal Variability in Disturbed and Undisturbed Rangelands

Current physically based overland flow erosion models for rangeland application do not separate disturbed and undisturbed conditions in modeling concentrated flow erosion. In this study, concentrated flow simulations on disturbed and undisturbed rangelands were used to estimate the erodibility and to evaluate the performance of linear and power law equations that describe the relationship between erosion rate and several hydraulic parameters. None of the hydraulic parameters consistently predicted the detachment capacity well for all sites, however, stream power performed better than most of other hydraulic parameters. Using power law functions did not improve the detachment relation with respect to that of the linear function. Concentrated flow erodibility increased significantly when a site was exposed to a disturbance such as fire or tree encroachment into sagebrush steppe. This study showed that burning increases erosion by amplifying the erosive power of overland flow through removing obstacles and by changing the soil properties affecting erodibility itself. However, the magnitude of fire impact varied among sites due to inherent differences in site characteristics and variability in burn severity. In most cases we observed concentrated flow erodibility had a high value at overland flow initiation and then started to decline with time due to reduction of sediment availability. Thus we developed an empirical function to predict erodibility variation within a runoff event as a function of cumulative unit discharge. Empirical equations were also developed to predict erodibility variation with time postdisturbance as a function of readily available vegetation cover and surface soil texture data

Red Queen Coevolution on Fitness Landscapes

Species do not merely evolve, they also coevolve with other organisms. Coevolution is a major force driving interacting species to continuously evolve ex- ploring their fitness landscapes. Coevolution involves the coupling of species fit- ness landscapes, linking species genetic changes with their inter-specific ecological interactions. Here we first introduce the Red Queen hypothesis of evolution com- menting on some theoretical aspects and empirical evidences. As an introduction to the fitness landscape concept, we review key issues on evolution on simple and rugged fitness landscapes. Then we present key modeling examples of coevolution on different fitness landscapes at different scales, from RNA viruses to complex ecosystems and macroevolution.Comment: 40 pages, 12 figures. To appear in "Recent Advances in the Theory and Application of Fitness Landscapes" (H. Richter and A. Engelbrecht, eds.). Springer Series in Emergence, Complexity, and Computation, 201

Incorporating Hydrologic Data and Ecohydrologic Relationships into Ecological Site Descriptions

The purpose of this paper is to recommend a framework and methodology for incorporating hydrologic data and ecohydrologic relationships in Ecological Site Descriptions (ESDs) and thereby enhance the utility of ESDs for assessing rangelands and guiding resilience-based management strategies. Resilience-based strategies assess and manage ecological state dynamics that affect state vulnerability and, therefore, provide opportunities to adapt management. Many rangelands are spatially heterogeneous or sparsely vegetated where the vegetation structure strongly influences infiltration and soil retention. Infiltration and soil retention further influence soil water recharge, nutrient availability, and overall plant productivity. These key ecohydrologic relationships govern the ecologic resilience of the various states and community phases on many rangeland ecological sites (ESs) and are strongly affected by management practices, land use, and disturbances. However, ecohydrologic data and relationships are often missing in ESDs and state-and-transition models (STMs). To address this void, we used literature to determine the data required for inclusion of key ecohydrologic feedbacks into ESDs, developed a framework and methodology for data integration within the current ESD structure, and applied the framework to a select ES for demonstrative purposes. We also evaluated the utility of the Rangeland Hydrology and Erosion Model (RHEM) for assessment and enhancement of ESDs based in part on hydrologic function. We present the framework as a broadly applicable methodology for integrating ecohydrologic relationships and feedbacks into ESDs and resilience-based management strategies. Our proposed framework increases the utility of ESDs to assess rangelands, target conservation and restoration practices, and predict ecosystem responses to management. The integration of RHEM technology and our suggested framework on ecohydrologic relations expands the ecological foundation of the overall ESD concept for rangeland management and is well aligned with resilience-based, adaptive management of US rangelands. The proposed enhancement of ESDs will improve communication between private land owners and resource managers and researchers across multiple disciplines in the field of rangeland management