Locating bugs without looking back

Bug localisation is a core program comprehension task in software maintenance: given the observation of a bug, e.g. via a bug report, where is it located in the source code? Information retrieval (IR) approaches see the bug report as the query, and the source code files as the documents to be retrieved, ranked by relevance. Such approaches have the advantage of not requiring expensive static or dynamic analysis of the code. However, current state-of-the-art IR approaches rely on project history, in particular previously fixed bugs or previous versions of the source code. We present a novel approach that directly scores each current file against the given report, thus not requiring past code and reports. The scoring method is based on heuristics identified through manual inspection of a small sample of bug reports. We compare our approach to eight others, using their own five metrics on their own six open source projects. Out of 30 performance indicators, we improve 27 and equal 2. Over the projects analysed, on average we find one or more affected files in the top 10 ranked files for 76% of the bug reports. These results show the applicability of our approach to software projects without history

How the vertebrates were made: selective pruning of a double-duplicated genome

Vertebrates are the result of an ancient double duplication of the genome. A new study published in BMC Biology explores the selective retention of genes after this event, finding an extensive enrichment of signaling proteins and transcription factors. Analysis of their expression patterns, interactions and subsequent history reflect the forces that drove their evolution, and with it the evolution of vertebrate complexity

Larval development of the pea crab Afropinnotheres monodi Manning, 1993 (Decapoda, Pinnotheridae) using plankton-collected and laboratory-reared specimens: effects of temperature

The aim of this study was to assess the effect of temperature on the survival and duration of larval development in the African pea crab Afropinnotheres monodi, as well as to describe its larval stages. We studied larvae reared in the laboratory and also specimens collected from plankton from the Gulf of Cádiz at two different temperatures. According to the results of this study, larval development of A. monodi involves four zoea stages and one megalopa and lasts around 25 days at 25°C, and longer than 40 days at 19°C. Such a temperature-related duration of this dispersive phase may be causing a higher recruitment to parental populations during the summer, but a higher dispersal to new locations during the rest of the year, a seasonal pattern of dispersion which could favour the successful expansion of this non-native species into European waters. The identification of both larval phases from plankton samples and adult specimens was carried out using morphological characters and molecular techniques. Both the 16S mtDNA sequences of this species, now available in GenBank, and the larval descriptions provided by this study could help to establish an early alert for the detection of this African species in its northward expansion

Digital technologies in the public-health response to COVID-19

Digital technologies are being harnessed to support the public-health response to COVID-19 worldwide, including population surveillance, case identification, contact tracing and evaluation of interventions on the basis of mobility data and communication with the public. These rapid responses leverage billions of mobile phones, large online datasets, connected devices, relatively low-cost computing resources and advances in machine learning and natural language processing. This Review aims to capture the breadth of digital innovations for the public-health response to COVID-19 worldwide and their limitations, and barriers to their implementation, including legal, ethical and privacy barriers, as well as organizational and workforce barriers. The future of public health is likely to become increasingly digital, and we review the need for the alignment of international strategies for the regulation, evaluation and use of digital technologies to strengthen pandemic management, and future preparedness for COVID-19 and other infectious diseases

Are mice good models for human neuromuscular disease? Comparing muscle excursions in walking between mice and humans

The mouse is one of the most widely used animal models to study neuromuscular diseases and test new therapeutic strategies. However, findings from successful pre-clinical studies using mouse models frequently fail to translate to humans due to various factors. Differences in muscle function between the two species could be crucial but often have been overlooked. The purpose of this study was to evaluate and compare muscle excursions in walking between mice and humans

Niche as a determinant of word fate in online groups

Patterns of word use both reflect and influence a myriad of human activities and interactions. Like other entities that are reproduced and evolve, words rise or decline depending upon a complex interplay between {their intrinsic properties and the environments in which they function}. Using Internet discussion communities as model systems, we define the concept of a word niche as the relationship between the word and the characteristic features of the environments in which it is used. We develop a method to quantify two important aspects of the size of the word niche: the range of individuals using the word and the range of topics it is used to discuss. Controlling for word frequency, we show that these aspects of the word niche are strong determinants of changes in word frequency. Previous studies have already indicated that word frequency itself is a correlate of word success at historical time scales. Our analysis of changes in word frequencies over time reveals that the relative sizes of word niches are far more important than word frequencies in the dynamics of the entire vocabulary at shorter time scales, as the language adapts to new concepts and social groupings. We also distinguish endogenous versus exogenous factors as additional contributors to the fates of words, and demonstrate the force of this distinction in the rise of novel words. Our results indicate that short-term nonstationarity in word statistics is strongly driven by individual proclivities, including inclinations to provide novel information and to project a distinctive social identity.Comment: Supporting Information is available here: http://www.plosone.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pone.0019009.s00

Impact of socio-economic deprivation on death rates after surgery for upper gastrointestinal tract cancer

We hypothesised that socio-economic deprivation in England may be a prognostic factor for death after oesophagectomy or gastrectomy for cancer of the upper gastrointestinal tract. We analysed statistical data from hospital records linked to death records for patients who underwent operations for oesophageal and gastric cancer in England from April 1998 to March 2002. The patients were stratified into quintiles according to the index of multiple deprivation (IMD) (2000) for their place (ward) of residence. Age and sex standardised death rates at 30 and 90 days for each deprivation quintile were calculated. Following oesophagectomy, death rates showed a significant association with IMD. They increased with increasing levels of deprivation: the odds ratio for death, comparing highest with lowest quintile for deprivation, was 1.37 (95% confidence interval 1.03–1.85) at 30 days and 1.30 (1.04–1.64) at 90 days. Following gastrectomy, the death rates showed smaller and nonsignificant associations with IMD with odds ratios of 1.16 (0.84–1.62) and 1.10 (0.86–1.41), respectively. There is a significant association between social deprivation and death after oesophagectomy, but less of an association, if any, after gastrectomy in current UK practice

Emergent complex neural dynamics

A large repertoire of spatiotemporal activity patterns in the brain is the basis for adaptive behaviour. Understanding the mechanism by which the brain's hundred billion neurons and hundred trillion synapses manage to produce such a range of cortical configurations in a flexible manner remains a fundamental problem in neuroscience. One plausible solution is the involvement of universal mechanisms of emergent complex phenomena evident in dynamical systems poised near a critical point of a second-order phase transition. We review recent theoretical and empirical results supporting the notion that the brain is naturally poised near criticality, as well as its implications for better understanding of the brain