The effectiveness of refactoring, based on a compatibility testing taxonomy and a dependency graph

In this paper, we describe and then appraise a testing taxonomy proposed by van Deursen and Moonen (VD&M) based on the post-refactoring repeatability of tests. Four categories of refactoring are identified by VD&M ranging from semantic-preserving to incompatible, where, for the former, no new tests are required and for the latter, a completely new test set has to be developed. In our appraisal of the taxonomy, we heavily stress the need for the inter-dependence of the refactoring categories to be considered when making refactoring decisions and we base that need on a refactoring dependency graph developed as part of the research. We demonstrate that while incompatible refactorings may be harmful and time-consuming from a testing perspective, semantic-preserving refactorings can have equally unpleasant hidden ramifications despite their advantages. In fact, refactorings which fall into neither category have the most interesting properties. We support our results with empirical refactoring data drawn from seven Java open-source systems (OSS) and from the same analysis form a tentative categorization of code smells

Available energy of the world ocean

The available energy of the ocean is the excess of the sum of the ocean\u27s internal and gravitational energies with respect to its equilibrium state, which is in thermodynamic equilibrium and has the same total entropy as the ocean. The equilibrium state for the world ocean is rigorously determined to be an isothermal ocean with a temperature of 3.66˚C and a horizontally uniform absolute salinity that increases monotonically from 27.30 g kg–1 at the surface to 47.39 g kg–1 at a depth of 5.5 km. This salinity profile is consistent with a uniform relative chemical potential of 47.44 J g–1 salt. The ocean\u27s available energy is 220 × 1021 J or 630 MJ m–2. Most (72%) of the available energy is due to the internal energy difference between the ocean and its equilibrium state; the remaining 28% is due to the gravitational energy difference. The ocean\u27s available energy is shown to be concentrated vertically in the upper half kilometer and geographically in the tropics and subtropics. This distribution is accurately represented by the temperature variance from the equilibrium temperature. The contributions of sea ice and variable sea surface height to the available energy are estimated to be small

Analysis of the mean annual cycle of the dissolved oxygen anomaly in the World Ocean

A global climatology of the dissolved oxygen anomaly (the excess over saturation) is created with monthly resolution in the upper 500 m of the ocean. The climatology is based on dissolved oxygen, temperature and salinity data archived at the National Oceanographic Data Center. Examination of this climatology reveals statistically significant annual cycles throughout the upper 500 m of the World Ocean, though seasonal variations are most coherent in the North Atlantic, where data density is greatest. Vertical trends in the phase and amplitude of the annual cycle are noted. The cycle in surface waters is characterized by a summer maximum and a winter minimum, consistent with warming and high rates of photosynthesis during the summer, and cooling and entrainment of oxygen-depleted water during the winter. In low and middle latitudes, the amplitude increases with depth and the maximum occurs later in the year, a trend consistent with the seasonal accumulation of oxygen associated with the shallow oxygen maximum. At a depth that varies between about 30 and 130 m, the phase of the annual cycle undergoes an abrupt shift. We call this depth the oxygen nodal depth. Below the nodal depth, the annual cycle is characterized by an early-spring maximum and a late-fall minimum, consistent with a cycle dominated by respiration during the spring and summer and replenishment of oxygen from the atmosphere by ventilation during the fall and winter. Below the nodal depth, the amplitude of the annual cycle generally decreases with depth, indicative of decreasing respiration and ventilation rates, or less seasonality in both processes. We postulate that the nodal depth in middle and high latitudes corresponds closely to the summertime compensation depth, where photosynthesis and net community respiration are equal. With this interpretation of the nodal depth and a simple model of the penetration of light in the water column, a compensation light intensity of 1 W m−2 (4μE m−2 s−1) is deduced, at the low end of independent estimates. Horizontal trends in the phase and amplitude of the annual cycle are also noted. We find that the nodal depth decreases toward the poles in both hemispheres and is generally greater in the Southern Hemisphere, patterns found to be consistent with light-based estimates of the compensation depth. The amplitude of the annual cycle in the oxygen anomaly increases monotonically with latitude, and higher latitudes lag lower latitudes. In the North Atlantic and North Pacific, the amplitude of the annual cycle tends to increase from east to west at all depths and latitudes, as expected considering that physical forcing has greater seasonal variability in the west. The tropics and the North Indian Ocean have features that distinguish them from other regions. Below about 75 m, these waters have pronounced annual cycles of the oxygen anomaly that are shown to be caused mainly by wind-driven adiabatic displacements of the thermocline. A semiannual cycle of the oxygen anomaly is found in the surface waters of the North Indian Ocean, consistent with the known semiannual cycle of surface heat flux in this region

Understanding Coastal Carbon Cycling by Linking Top- Down and Bottom-Up Approaches

The coastal zone, despite occupying a small fraction of the Earth\u27s surface area, is an important component of the global carbon (C) cycle. Coastal wetlands, including mangrove forests, tidal marshes, and seagrass meadows, compose a domain of large reservoirs of biomass and soil C [Fourqurean et al., 2012; Donato et al., 2011; Pendleton et al., 2012; Regnier et al., 2013; Bauer et al.,2013]. These wetlands and their associated C reservoirs (2 to 25 petagrams C; best estimate of 7 petagrams C [Pendleton et al., 2012]) provide numerous ecosystem services and serve as key links between land and ocean

Photochemistry, mixing and diurnal cycles in the upper ocean

The interplay between ocean photochemistry and surface boundary-layer physics is explored in a range of analytical and numerical process models. For simple systems, key attributes of the photochemical distribution—diurnal cycle, surface concentration, and the bulk concentration difference across the “mixed layer”—can be expressed in terms of a small number of physical (vertical diffusivity) and photochemical (turnover timescale and production depth scale) scaling factors. A coupled, 1-D photochemical/physical model is used to examine the more general case with finite mixing rates, variable photochemical production and evolving boundary layer depth. Finite boundary layer mixing rates act to increase both the diurnal cycle and mean concentration at the surface. The diurnal cycle and mean surface concentration are further amplified by coupling between photochemistry and diurnal physics. The daily heating/cooling cycle of the upper ocean can lead to a significant reduction in mixing and boundary-layer depth during the day when photochemical production is at a maximum. Accounting for these effects results in additional surface trapping of photochemically produced species and significant enhancements of the surface diurnal cycle and daily mean. The implications of our model results for field data interpretation and global air-sea flux calculations are also discussed

Reply to "Comment on `Lattice determination of Sigma - Lambda mixing' "

In this Reply, we respond to the above Comment. Our computation [Phys. Rev. D 91 (2015) 074512] only took into account pure QCD effects, arising from quark mass differences, so it is not surprising that there are discrepancies in isospin splittings and in the Sigma - Lambda mixing angle. We expect that these discrepancies will be smaller in a full calculation incorporating QED effects.Comment: 5 page

Shallow Remineralization in the Sargasso Sea Estimated from Seasonal Variations in Oxygen and Dissolved Inorganic Carbon

A diagnostic model of the mean annual cycles of dissolved inorganic carbon (DIC) and oxygen below the mixed layer at the Bermuda Atlantic Time-series Study (BATS) site is presented and used to estimate organic carbon remineralization in the seasonal thermocline. The model includes lateral and vertical advection as well as vertical, diffusion. Very good agreement is found for the remineralization estimates based on oxygen and DIC. Net remineralization averaged from mid-spring to early fall is found to be a maximum between 120 and 140 in. Remineralization integrated between 100 (the compensation depth) and 250 m during this period is estimated to be about 1 mol C/sq m. This flux is consistent with independent estimates of the loss of particulate and dissolved organic carbon