Analyzing Software Evolution through Feature Views

Features encapsulate the domain knowledge of a software system and thus are valuable sources of information for a reverse engineer. When analyzing the evolution of a system, we need to know how and which features were modified to recover both the change intention and its extent, namely which source artifacts are affected. Typically, the implementation of a feature crosscuts a number of source artifacts. To obtain a mapping between features to the source artifacts, we exercise the features and capture their execution traces. However this results in large traces that are difficult to interpret. To tackle this issue we compact the traces into simple sets of source artifacts that participate in a feature's runtime behavior. We refer to these compacted traces as feature views. Within a feature view, we partition the source artifacts into disjoint sets of characterized software entities. The characterization defines the level of participation of a source entity in the features. We then analyze the features over several versions of a system and we plot their evolution to reveal how and hich features were affected by changes in the code. We show the usefulness of our approach by applying it to a case study where we address the problem of merging parallel development tracks of the same system.

The Ecological Significance of the Herbaceous Layer in Temperate Forest Ecosystems

Despite a growing awareness that the herbaceous layer serves a special role in maintaining the structure and function of forests, this stratum remainsan underappreciated aspect of forest ecosystems. In this article I review and synthesize information concerning the herb layer’s structure,composition, and dynamics to emphasize its role as an integral component of forest ecosystems. Because species diversity is highest in the herb layeramong all forest strata, forest biodiversity is largely a function of the herb-layer community. Competitive interactions within the herb layer candetermine the initial success of plants occupying higher strata, including the regeneration of dominant overstory tree species. Furthermore, the herblayer and the overstory can become linked through parallel responses to similar environmental gradients. These relationships between strata varyboth spatially and temporally. Because the herb layer responds sensitively to disturbance across broad spatial and temporal scales, its dynamics canprovide important information regarding the site characteristics of forests, including patterns of past land-use practices. Thus, the herb layer has asignificance that belies its diminutive stature.

The discovery of new 11beta-hydroxysteroid dehydrogenase type 1 inhibitors by common feature pharmacophore modeling and virtual screening

11beta-Hydroxysteroid dehydrogenase (11beta-HSD) enzymes catalyze the conversion of biologically inactive 11-ketosteroids into their active 11beta-hydroxy derivatives and vice versa. Inhibition of 11beta-HSD1 has considerable therapeutic potential for glucocorticoid-associated diseases including obesity, diabetes, wound healing, and muscle atrophy. Because inhibition of related enzymes such as 11beta-HSD2 and 17beta-HSDs causes sodium retention and hypertension or interferes with sex steroid hormone metabolism, respectively, highly selective 11beta-HSD1 inhibitors are required for successful therapy. Here, we employed the software package Catalyst to develop ligand-based multifeature pharmacophore models for 11beta-HSD1 inhibitors. Virtual screening experiments and subsequent in vitro evaluation of promising hits revealed several selective inhibitors. Efficient inhibition of recombinant human 11beta-HSD1 in intact transfected cells as well as endogenous enzyme in mouse 3T3-L1 adipocytes and C2C12 myotubes was demonstrated for compound 27, which was able to block subsequent cortisol-dependent activation of glucocorticoid receptors with only minor direct effects on the receptor itself. Our results suggest that inhibitor-based pharmacophore models for 11beta-HSD1 in combination with suitable cell-based activity assays, including such for related enzymes, can be used for the identification of selective and potent inhibitors.

Livelihoods in Transition: Changing Land Use Strategies and Ecological Implications in a Post Soviet Setting (Kyrgyzstan)

The sudden independence of Kyrgyzstan from the Soviet Union in 1991 led to a total rupture of industrial and agricultural production. Based on empirical data, this study seeks to identify key land use transformation processes since the late 1980s, their impact on people's livelihoods and the implication for natural resources in the communes of Tosh Bulak and Saz, located in the Sokuluk River Basin on the northern slope of the Kyrgyz Range. Using the concept of the sustainable livelihood approach as an analytical framework, three different livelihood strategies were identified: (1) An accumulation strategy applied by wealthy households where renting and/or buying of land is a key element; they are the only household category capable of venturing into rain fed agriculture. (2) A preserving strategy involving mainly intermediate households who are not able to buy or rent additional agricultural land; very often they are forced to return their land to the commune or sell it to wealthier households. (3) A coping strategy including mainly poor households consisting of elderly pensioners or headed by single mothers; due to their limited labour and economic power, agricultural production is very low and hardly covers subsistence needs; pensions and social allowances form the backbone of these livelihoods. Ecological assessments have shown that the forage productivity of remote high mountain pastures has increased from 5 to 22 per cent since 1978. At the same time forage productivity on pre-mountain and mountain pastures close to villages has generally decreased from 1 to 34 per cent. It seems that the main avenues for livelihoods to increase their wealth are to be found in the agricultural sector by controlling more and mainly irrigated land as well as by increasing livestock. The losers in this process are thus those households unable to keep or exploit their arable land or to benefit from new agricultural land. Ensuring access to land for the poor is therefore imperative in order to combat rural poverty and socio-economic disparities in rural Kyrgyzstan.

Ecological study of the predictors of successful management of dyslipidemia in HIV-infected patients on ART: the Swiss HIV Cohort Study

PURPOSE: Antiretroviral therapy (ART) may induce metabolic changes and increase the risk of coronary heart disease (CHD). Based on a health care system approach, we investigated predictors for normalization of dyslipidemia in HIV-infected individuals receiving ART. METHOD: Individuals included in the study were registered in the Swiss HIV Cohort Study (SHCS), had dyslipidemia but were not on lipid-lowering medication, were on potent ART for >or= 3 months, and had >or= 2 follow-up visits. Dyslipidemia was defined as two consecutive total cholesterol (TC) values above recommended levels. Predictors of achieving treatment goals for TC were assessed using Cox models. RESULTS: Analysis included 958 individuals with median followup of 2.3 years (IQR 1.2-4.0). 454 patients (47.4%) achieved TC treatment goals. In adjusted analyses, variables significantly associated with a lower hazard of reaching TC treatment goals were as follows: older age (compared to 18-37 year olds: hazard ratio [HR] 0.62 for 45-52 year olds, 95% CI 0.47-0.82; HR 0.40 for 53-85, 95% CI 0.29-0.54), diabetes (HR 0.39, 95% CI 0.26-0.59), history of coronary heart disease (HR 0.27, 95% CI 0.10-0.71), higher baseline TC (HR 0.78, 95% CI 0.71-0.85), baseline triple nucleoside regimen (HR 0.12 compared to PI-only regimen, 95% CI 0.07-0.21), longer time on PI-only regimen (HR 0.39, 95% CI 0.33-0.46), longer time on NNRTI only regimen (HR 0.35, 95% CI 0.29-0.43), and longer time on PI/NNRTI regimen (HR 0.34, 95% CI 0.26-0.43). Switching ART regimen when viral load was undetectable was associated with a higher hazard of reaching TC treatment goals (HR 1.48, 95% CI 1.14-1.91). CONCLUSION: In SHCS participants on ART, several ART-related and not ART-related epidemiological factors were associated with insufficient control of dyslipidemia. Control of dyslipidemia in ART recipients must be further improved.