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

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

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

A lattice determination of Sigma - Lambda mixing

Isospin breaking effects in baryon octet (and decuplet) masses are due to a combination of up and down quark mass differences and electromagnetic effects and lead to small mass splittings. Between the Sigma and Lambda this mass splitting is much larger, this being mostly due to their different wavefunctions. However when isospin is broken, there is a mixing between between these states. We describe the formalism necessary to determine the QCD mixing matrix and hence find the mixing angle and mass splitting between the Sigma and Lambda particles due to QCD effects.Comment: 40 pages, 5 figures, published versio

Dissolution of calcium carbonate: observations and model results in the North Atlantic

International audienceWe investigate the significance of in situ dissolution of calcium carbonate above its saturation horizons. The study relies on observations from the open subpolar North Atlantic [sNA] and on a 3-D biogeochemical model. The sNA is particularly well suited for observation-based detections of in situ, i.e. shallow depth CaCO3 dissolution [SDCCD] as it is a region of high CaCO3 production, deep CaCO3 saturation horizons, and precisely-defined pre-formed alkalinity. Based on the analysis of a comprehensive alkalinity data set we find that SDCCD does not appear to be a significant process in the open sNA. The results from the model support the observational findings and do not indicate a significant need of SDCCD to explain observed patterns of alkalinity in the North Atlantic. Instead our investigation points to the importance of mixing processes for the redistribution of alkalinity from dissolution of CaCO3 from below its saturation horizons. However, mixing has recently been neglected for a number of studies that called for SDCCD in the sNA and on global scale

Potential climate-change impacts on the Chesapeake Bay

We review current understanding of the potential impact of climate change on the Chesapeake Bay. Scenarios for CO2 emissions indicate that by the end of the 21st century the Bay region will experience significant changes in climate forcings with respect to historical conditions, including increases in CO2 concentrations, sea level, and water temperature of 50–160%, 0.7–1.6m, and 2–6C, respectively. Also likely are increases in precipitation amount (very likely in the winter and spring), precipitation intensity, intensity of tropical and extratropical cyclones (though their frequency may decrease), and sea-level variability. The greatest uncertainty is associatedwith changes in annual streamflow, though it is likely that winter and spring flows will increase. Climate change alone will cause the Bay to function very differently in the future. Likely changes include: (1) an increase in coastal flooding and submergence of estuarine wetlands; (2) an increase in salinity variability on many time scales; (3) an increase in harmful algae; (4) an increase in hypoxia; (5) a reduction of eelgrass, the dominant submergedaquatic vegetation in the Bay; and (6) altered interactions among trophic levels, with subtropical fish and shellfish species ultimately being favored in the Bay. The magnitude of these changes is sensitive to the CO2 emission trajectory, so that actions taken now to reduce CO2 emissions will reduce climate impacts on the Bay. Research needs include improved precipitation and streamflow projections for the Bay watershed and whole-system monitoring, modeling, and process studies that can capture the likely non-linear responses of the Chesapeake Bay system to climate variability, climate change, and their interaction with other anthropogenic stressor

Dissolution of calcium carbonate: observations and model results in the subpolar North Atlantic

We investigate the significance of in situ dissolution of calcium carbonate above its saturation horizons using observations from the open subpolar North Atlantic [sNA] and to a lesser extent a 3-D biogeochemical model. The sNA is particularly well suited for observation-based detections of in situ, i.e. shallow-depth CaCO3 dissolution [SDCCD] as it is a region of high CaCO3 production, deep CaCO3 saturation horizons, and precisely-defined pre-formed alkalinity. Based on the analysis of a comprehensive alkalinity data set we find that SDCCD does not appear to be a significant process in the open sNA. The results from the model support the observational findings by indicating that there is not a significant need of SDCCD to explain observed patterns of alkalinity in the North Atlantic. Instead our investigation points to the importance of mixing processes for the redistribution of alkalinity from dissolution of CaCO3 from below its saturation horizons. However, mixing has recently been neglected for a number of studies that called for SDCCD in the sNA and on global scale

High-frequency CO2-system variability over the winter-to-spring transition in a large coastal plain estuary

Understanding the vulnerability of estuarine ecosystems to anthropogenic impacts requires a quantitative assessment of the dynamic drivers of change to the carbonate (CO2) system. Here we present new high‐frequency pH data from a moored sensor. These data are combined with discrete observations to create continuous time series of total dissolved inorganic carbon (TCO2), CO2 partial pressure (pCO2), and carbonate saturation state. We present two deployments over the winter‐to‐spring transition in the lower York River (where it meets the Chesapeake Bay mainstem) in 2016/2017 and 2017/2018. TCO2 budgets with daily resolution are constructed, and contributions from circulation, air‐sea CO2 exchange, and biology are quantified. We find that TCO2 is most strongly influenced by circulation and biological processes; pCO2 and pH also respond strongly to changes in temperature. The system transitions from autotrophic to heterotrophic conditions multiple times during both deployments; the conventional view of a spring bloom and subsequent summer production followed by autumn and winter respiration may not apply to this region. Despite the dominance of respiration in winter and early spring, surface waters were undersaturated with respect to atmospheric CO2 for the majority of both deployments with mean fluxes ranging from −9 to −5 mmol C·m−2·day−1. Deployments a year apart indicate that the seasonal transition in the CO2 system differs significantly from one year to the next and highlights the necessity of sustained monitoring in dynamic nearshore environments