Detecting and escaping infinite loops with jolt

25th European Conference, Lancaster, Uk, July 25-29, 2011 ProceedingsInfinite loops can make applications unresponsive. Potential problems include lost work or output, denied access to application functionality, and a lack of responses to urgent events. We present Jolt, a novel system for dynamically detecting and escaping infinite loops. At the user’s request, Jolt attaches to an application to monitor its progress. Specifically, Jolt records the program state at the start of each loop iteration. If two consecutive loop iterations produce the same state, Jolt reports to the user that the application is in an infinite loop. At the user’s option, Jolt can then transfer control to a statement following the loop, thereby allowing the application to escape the infinite loop and ideally continue its productive execution. The immediate goal is to enable the application to execute long enough to save any pending work, finish any in-progress computations, or respond to any urgent events. We evaluated Jolt by applying it to detect and escape eight infinite loops in five benchmark applications. Jolt was able to detect seven of the eight infinite loops (the eighth changes the state on every iteration). We also evaluated the effect of escaping an infinite loop as an alternative to terminating the application. In all of our benchmark applications, escaping an infinite loop produced a more useful output than terminating the application. Finally, we evaluated how well escaping from an infinite loop approximated the correction that the developers later made to the application. For two out of our eight loops, escaping the infinite loop produced the same output as the corrected version of the application

Active Layer Groundwater Flow: The Interrelated Effects of Stratigraphy, Thaw, and Topography

The external drivers and internal controls of groundwater flow in the thawed “active layer” above permafrost are poorly constrained because they are dynamic and spatially variable. Understanding these controls is critical because groundwater can supply solutes such as dissolved organic matter to surface water bodies. We calculated steady‐state three‐dimensional suprapermafrost groundwater flow through the active layer using measurements of aquifer geometry, saturated thickness, and hydraulic properties collected from two major landscape types over time within a first‐order Arctic watershed. The depth position and thickness of the saturated zone is the dominant control of groundwater flow variability between sites and during different times of year. The effect of water table depth on groundwater flow dwarfs the effect of thaw depth. In landscapes with low land‐surface slopes (2–4%), a combination of higher water tables and thicker, permeable peat deposits cause relatively constant groundwater flows between the early and late thawed seasons. Landscapes with larger land‐surface slopes (4–10%) have both deeper water tables and thinner peat deposits; here the commonly observed permeability decrease with depth is more pronounced than in flatter areas, and groundwater flows decrease significantly between early and late summer as the water table drops. Groundwater flows are also affected by microtopographic features that retain groundwater that could otherwise be released as the active layer deepens. The dominant sources of groundwater, and thus dissolved organic matter, are likely wet, flatter regions with thick organic layers. This finding informs fluid flow and solute transport dynamics for the present and future Arctic.Plain Language SummaryGroundwater flow in permafrost watersheds is potentially a key component of global carbon budgets because permafrost soil stores vast amounts of carbon that could be mobilized due to a warming climate and the corresponding increase in soil thaw. In addition to carrying carbon, groundwater can supply important nutrients and solutes to surface waters. However, we do not yet understand the factors that control groundwater flow in soils above permafrost because saturation changes rapidly and continuously, and soil hydraulic properties are largely unknown. We created measurement‐informed calculations of groundwater flow from areas of permafrost with different characteristics and found that soil types, which vary based on the slope of the land surface, are the most important control. Near‐surface soils were identical in hillslopes and valleys, whereas deeper soils in hillslopes allowed for less groundwater flow than in valleys. In early summer, when only the near‐surface soils were thawed, groundwater flows in the hillslopes and valley were similar. In late summer, when the deeper soil was thawed, groundwater flow in the valley remained high, but flow in the hillslope was negligible. Our observations also showed that small mounds on the land surface caused groundwater to be trapped behind underground ice dams.Key PointsDetailed measurements of hydraulic head, hydraulic conductivity, and saturated thicknesses in active layers were made over time and spaceThree main soil layers consistently comprise the stratigraphy of the active layer across the studied Arctic watershedGroundwater flow depends most on the depth of the water table and the subsurface stratigraphy, which varies based on landscape typePeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151862/1/wrcr24085_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151862/2/wrcr24085.pd

Active Layer Groundwater Flow: The Interrelated Effects of Stratigraphy, Thaw, and Topography

The external drivers and internal controls of groundwater flow in the thawed “active layer” above permafrost are poorly constrained because they are dynamic and spatially variable. Understanding these controls is critical because groundwater can supply solutes such as dissolved organic matter to surface water bodies. We calculated steady‐state three‐dimensional suprapermafrost groundwater flow through the active layer using measurements of aquifer geometry, saturated thickness, and hydraulic properties collected from two major landscape types over time within a first‐order Arctic watershed. The depth position and thickness of the saturated zone is the dominant control of groundwater flow variability between sites and during different times of year. The effect of water table depth on groundwater flow dwarfs the effect of thaw depth. In landscapes with low land‐surface slopes (2–4%), a combination of higher water tables and thicker, permeable peat deposits cause relatively constant groundwater flows between the early and late thawed seasons. Landscapes with larger land‐surface slopes (4–10%) have both deeper water tables and thinner peat deposits; here the commonly observed permeability decrease with depth is more pronounced than in flatter areas, and groundwater flows decrease significantly between early and late summer as the water table drops. Groundwater flows are also affected by microtopographic features that retain groundwater that could otherwise be released as the active layer deepens. The dominant sources of groundwater, and thus dissolved organic matter, are likely wet, flatter regions with thick organic layers. This finding informs fluid flow and solute transport dynamics for the present and future Arctic

Groundwater Flow and Exchange Across the Land Surface Explain Carbon Export Patterns in Continuous Permafrost Watersheds

Groundwater flow regimes in the seasonally thawed soils in areas of continuous permafrost are relatively unknown despite their potential role in delivering water, carbon, and nutrients to streams. Using numerical groundwater flow models informed by observations from a headwater catchment in arctic Alaska, United States, we identify several mechanisms that result in substantial surface‐subsurface water exchanges across the land surface during downslope transport and create a primary control on dissolved organic carbon loading to streams and rivers. The models indicate that surface water flowing downslope has a substantial groundwater component due to rapid surface‐subsurface exchanges across a range of hydrologic states, from unsaturated to flooded. Field‐based measurements corroborate the high groundwater contributions, and river dissolved organic carbon concentrations are similar to that of groundwater across large discharge ranges. The persistence of these groundwater contributions in arctic watersheds will influence carbon export to rivers as thaw depth increases in a warmer climate

Groundwater Flow and Exchange Across the Land Surface Explain Carbon Export Patterns in Continuous Permafrost Watersheds

Groundwater flow regimes in the seasonally thawed soils in areas of continuous permafrost are relatively unknown despite their potential role in delivering water, carbon, and nutrients to streams. Using numerical groundwater flow models informed by observations from a headwater catchment in arctic Alaska, United States, we identify several mechanisms that result in substantial surface‐subsurface water exchanges across the land surface during downslope transport and create a primary control on dissolved organic carbon loading to streams and rivers. The models indicate that surface water flowing downslope has a substantial groundwater component due to rapid surface‐subsurface exchanges across a range of hydrologic states, from unsaturated to flooded. Field‐based measurements corroborate the high groundwater contributions, and river dissolved organic carbon concentrations are similar to that of groundwater across large discharge ranges. The persistence of these groundwater contributions in arctic watersheds will influence carbon export to rivers as thaw depth increases in a warmer climate

Empirical Models for Predicting Water and Heat Flow Properties of Permafrost Soils

Warming and thawing in the Arctic are promoting biogeochemical processing and hydrologic transport in carbon‐rich permafrost and soils that transfer carbon to surface waters or the atmosphere. Hydrologic and biogeochemical impacts of thawing are challenging to predict with sparse information on arctic soil hydraulic and thermal properties. We developed empirical and statistical models of soil properties for three main strata in the shallow, seasonally thawed soils above permafrost in a study area of ~7,500 km2 in Alaska. The models show that soil vertical stratification and hydraulic properties are predictable based on vegetation cover and slope. We also show that the distinct hydraulic and thermal properties of each soil stratum can be predicted solely from bulk density. These findings fill the gap for a sparsely mapped region of the Arctic and enable regional interpolation of soil properties critical for determining future hydrologic responses and the fate of carbon in thawing permafrost

Normalization anomalies in level truncation calculations

We test oscillator level truncation regularization in string field theory by calculating descent relations among vertices, or equivalently, the overlap of wedge states. We repeat the calculation using bosonic, as well as fermionic ghosts, where in the bosonic case we do the calculation both in the discrete and in the continuous basis. We also calculate analogous expressions in field level truncation. Each calculation gives a different result. We point out to the source of these differences and in the bosonic ghost case we pinpoint the origin of the difference between the discrete and continuous basis calculations. The conclusion is that level truncation regularization cannot be trusted in calculations involving normalization of singular states, such as wedge states, rank-one squeezed state projectors and string vertices.Comment: 1+20 pages, 6 figures. v2: Ref. added, typos correcte

Novel mutations expand the clinical spectrum of DYNC1H1-associated spinal muscular atrophy

OBJECTIVE To expand the clinical phenotype of autosomal dominant congenital spinal muscular atrophy with lower extremity predominance (SMA-LED) due to mutations in the dynein, cytoplasmic 1, heavy chain 1 (DYNC1H1) gene. METHODS Patients with a phenotype suggestive of a motor, non-length-dependent neuronopathy predominantly affecting the lower limbs were identified at participating neuromuscular centers and referred for targeted sequencing of DYNC1H1. RESULTS We report a cohort of 30 cases of SMA-LED from 16 families, carrying mutations in the tail and motor domains of DYNC1H1, including 10 novel mutations. These patients are characterized by congenital or childhood-onset lower limb wasting and weakness frequently associated with cognitive impairment. The clinical severity is variable, ranging from generalized arthrogryposis and inability to ambulate to exclusive and mild lower limb weakness. In many individuals with cognitive impairment (9/30 had cognitive impairment) who underwent brain MRI, there was an underlying structural malformation resulting in polymicrogyric appearance. The lower limb muscle MRI shows a distinctive pattern suggestive of denervation characterized by sparing and relative hypertrophy of the adductor longus and semitendinosus muscles at the thigh level, and diffuse involvement with relative sparing of the anterior-medial muscles at the calf level. Proximal muscle histopathology did not always show classic neurogenic features. CONCLUSION Our report expands the clinical spectrum of DYNC1H1-related SMA-LED to include generalized arthrogryposis. In addition, we report that the neurogenic peripheral pathology and the CNS neuronal migration defects are often associated, reinforcing the importance of DYNC1H1 in both central and peripheral neuronal functions

On surface states and star-subalgebras in string field theory

We elaborate on the relations between surface states and squeezed states. First, we investigate two different criteria for determining whether a matter sector squeezed state is also a surface state and show that the two criteria are equivalent. Then, we derive similar criteria for the ghost sector. Next, we refine the criterion for determining whether a surface state is in H_{\kappa^2}, the subalgebra of squeezed states obeying [S,K_1^2]=0. This enables us to find all the surface states of the H_{\kappa^2} subalgebra, and show that it consists only of wedge states and (hybrid) butterflies. Finally, we investigate generalizations of this criterion and find an infinite family of surface states subalgebras, whose surfaces are described using a "generalized Schwarz-Christoffel" mapping.Comment: 38 pages, 6 figures, JHEP style; typos corrected, ref. adde

Standardized research protocols enable transdisciplinary research of climate variation impacts in corn production systems

The important questions about agriculture, climate, and sustainability have become increasingly complex and require a coordinated, multifaceted approach for developing new knowledge and understanding. A multistate, transdisciplinary project was begun in 2011 to study the potential for both mitigation and adaptation of corn-based cropping systems to climate variations. The team is measuring the baseline as well as change of the system\u27s carbon (C), nitrogen (N), and water footprints, crop productivity, and pest pressure in response to existing and novel production practices. Nine states and 11 institutions are participating in the project, necessitating a well thought out approach to coordinating field data collection procedures at 35 research sites. In addition, the collected data must be brought together in a way that can be stored and used by persons not originally involved in the data collection, necessitating robust procedures for linking metadata with the data and clearly delineated rules for use and publication of data from the overall project. In order to improve the ability to compare data across sites and begin to make inferences about soil and cropping system responses to climate across the region, detailed research protocols were developed to standardize the types of measurements taken and the specific details such as depth, time, method, numbers of samples, and minimum data set required from each site. This process required significant time, debate, and commitment of all the investigators involved with field data collection and was also informed by the data needed to run the simulation models and life cycle analyses. Although individual research teams are collecting additional measurements beyond those stated in the standardized protocols, the written protocols are used by the team for the base measurements to be compared across the region. A centralized database was constructed to meet the needs of current researchers on this project as well as for future use for data synthesis and modeling for agricultural, ecosystem, and climate sciences