What is the Connection Between Issues, Bugs, and Enhancements? (Lessons Learned from 800+ Software Projects)

Agile teams juggle multiple tasks so professionals are often assigned to multiple projects, especially in service organizations that monitor and maintain a large suite of software for a large user base. If we could predict changes in project conditions changes, then managers could better adjust the staff allocated to those projects.This paper builds such a predictor using data from 832 open source and proprietary applications. Using a time series analysis of the last 4 months of issues, we can forecast how many bug reports and enhancement requests will be generated next month. The forecasts made in this way only require a frequency count of this issue reports (and do not require an historical record of bugs found in the project). That is, this kind of predictive model is very easy to deploy within a project. We hence strongly recommend this method for forecasting future issues, enhancements, and bugs in a project.Comment: Accepted to 2018 International Conference on Software Engineering, at the software engineering in practice track. 10 pages, 10 figure

ACUTE SPATIOTEMPORAL AND MUSCLE EXCITATION REPONSES TO WEARABLE LOWER LIMB LOADING DURING MAXIMAL VELOCITY SPRINTING

This study quantified the mechanical effects of adding light wearable loads to the thigh or shank segments during maximal velocity sprinting. Eight university level sprinters performed two 40 m sprints under each condition (unloaded, thigh loaded, shank loaded) in a randomised order, and effects were analysed using magnitude based inferences. In both loaded conditions, there was a possibly small decrease in step velocity which was associated with a likely small decrease in step rate and no clear difference in step length. There was a likely small increase in contact time in the thigh-loaded condition, and possibly small increases in both flight and contact time in the shank-loaded condition. There were no clear differences in biceps femoris or semitendinosus excitation between any conditions. These results provide information which can be used to objectively implement wearable resistance in to periodised training programmes

Size at birth, growth trajectory in early life, and cardiovascular and metabolic risks in early adulthood: EPICure study.

OBJECTIVE: To investigate whether size at birth and growth trajectories in infancy and childhood are associated with determinants of cardiovascular and metabolic risks in young adults born extremely preterm (EP, <26 weeks of gestation). METHODS: We used longitudinal data from the EPICure study of 129 EP survivors up to 19 years in the UK and Ireland in 1995. Determinants of cardiovascular and metabolic risks at 19 years included the presence of metabolic syndrome, body mass index (BMI) and systolic blood pressure (SBP). Predictors were birth weight for gestation and gain in weight z-scores in the following periods: birth-postmenstrual age of 40 weeks (term), infancy (term-2.5 years), early childhood (2.5-6.0 years) and late childhood (6-11 years). RESULTS: Metabolic syndrome was present in 8.7% of EP participants at 19 years. Compared with subjects without metabolic syndrome, those with metabolic syndrome tended to have a smaller size at birth (difference in means: -0.55 SD, 95% CI -1.10 to 0.01, p=0.053) and a greater increase in weight z-scores from term to 2.5 years (difference in means: 1.00 SD, 95% CI -0.17 to 2.17, p=0.094). BMI at 19 years was positively related to growth from 2.5 to 6.0 years (β: 1.03, 95% CI 0.31 to 1.75, p=0.006); an inverse association with birthweight z-scores was found in the lower socioeconomic status group (β: -1.79, 95% CI -3.41 to -0.17, p=0.031). Central SBP was positively related to growth from 2.5 to 6.0 years (β: 1.75, 95% CI 0.48 to 3.02, p=0.007). CONCLUSION: Size at EP birth and increased catch-up in weight from 2.5 to 6.0 years were associated with BMI and central SBP in early adulthood

Assignment of the four disulfides in the N-terminal somatomedin B domain of native vitronectin isolated from human plasma

The primary sequence of the N-terminal somatomedin B (SMB) domain of native vitronectin contains 44 amino acids, including a framework of four disulfide bonds formed by 8 closely spaced cysteines in sequence patterns similar to those found in the cystine knot family of proteins. The SMB domain of vitronectin was isolated by digesting the protein with endoproteinase Glu-C and purifying the N-terminal 1-55 peptide by reverse-phase high performance liquid chromatography. Through a combination of techniques, including stepwise reduction and alkylation at acidic pH, peptide mapping with matrix-assisted laser desorption ionization mass spectrometry and NMR, the disulfide bonds contained in the SMB domain have been determined to be Cys5:Cys9, Cys 19:Cys31, Cys21:Cys32, and Cys 25:Cys39. This pattern of disulfides differs from two other connectivities that have been reported previously for recombinant forms of the SMB domain expressed in Escherichia coli. This arrangement of disulfide bonds in the SMB domain from native vitronectin forms a rigid core around the Cys19: Cys31 and Cys21:Cys32 disulfides. A small positively charged loop is created at the N terminus by the Cys5: Cys9 cystine. The most prominent feature of this disulfide-bonding pattern is a loop between Cys25 and Cys 39 similar to cystine-stabilized α-helical structures commonly observed in cystine knots. This α-helix has been confirmed in the solution structure determined for this domain using NMR (Mayasundari, A., Whittemore, N. A., Serpersu, E. H., and Peterson, C. B. (2004) J. Biol. Chem. 279, 29359-29366). It confers function on the SMB domain, comprising the site for binding to plasminogen activator inhibitor type-1 and the urokinase receptor

Evolution of Male-Killer Suppression in a Natural Population

Male-killing bacteria are widespread in arthropods, and can profoundly alter the reproductive biology of their host species. Here we detail the first case of complete suppression of a male killer. The nymphalid butterfly Hypolimnas bolina is infected with a strain of the bacterium Wolbachia, wBol1, which kills male host embryos in Polynesian populations, but does not do so in many areas of Southeast Asia, where both males and female adults are naturally infected, and wBol1-infected females produce a 1:1 sex ratio. We demonstrate that absence of male killing by wBol1 is associated with dominant zygotic suppression of the action of the male killer. Simulations demonstrate host suppressors of male-killer action can spread very rapidly, and historical data indicating the presence of male killing in Southeast Asia in the very recent past suggests suppressor spread has been a very recent occurrence. Thus, male killer/host interactions are much more dynamic than previously recognised, with rapid and dramatic loss of the phenotype. Our results also indicate that suppression can render male killers completely quiescent, leading to the conclusion that some species that do not currently express a male killer may have done so in the past, and thus that more species have had their biology affected by these parasites than previously believed

The joint evolutionary histories of Wolbachia and mitochondria in Hypolimnas bolina

Background. The interaction between the Blue Moon butterfly, Hypolimnas bolina, and Wolbachia has attracted interest because of the high prevalence of male-killing achieved within the species, the ecological consequences of this high prevalence, the intensity of selection on the host to suppress the infection, and the presence of multiple Wolbachia infections inducing different phenotypes. We examined diversity in the co-inherited marker, mtDNA, and the partitioning of this between individuals of different infection status, as a means to investigate the population biology and evolutionary history of the Wolbachia infections. Results. Part of the mitochondrial COI gene was sequenced from 298 individuals of known infection status revealing ten different haplotypes. Despite very strong biological evidence that the sample represents a single species, the ten haplotypes did not fall within a monophyletic clade within the Hypolimnas genus, with one haplotype differing by 5% from the other nine. There were strong associations between infection status and mtDNA haplotype. The presence of wBol1 infection in association with strongly divergent haplotypes prompted closer examination of wBol1 genetic variation. This revealed the existence of two cryptic subtypes, wBol1a and wBol1b. The wBol1a infection, by far the most common, was in strict association with the single divergent mtDNA haplotype. The wBol1b infection was found with two haplotypes that were also observed in uninfected specimens. Finally, the wBol2 infection was associated with a large diversity of mtDNA haplotypes, most often shared with uninfected sympatric butterflies. Conclusion. This data overall supports the hypothesis that high prevalence of male-killing Wolbachia (wBol1) in H. bolina is associated with very high transmission efficiency rather than regular horizontal transmission. It also suggests this infection has undergone a recent selective sweep and was introduced in this species through introgression. In contrast, the sharing of haplotypes between wBol2-infected and uninfected individuals indicates that this strain is not perfectly transmitted and/or shows a significant level of horizontal transmission

Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation.

UnlabelledSyntrophus aciditrophicus is a model syntrophic bacterium that degrades key intermediates in anaerobic decomposition, such as benzoate, cyclohexane-1-carboxylate, and certain fatty acids, to acetate when grown with hydrogen-/formate-consuming microorganisms. ATP formation coupled to acetate production is the main source for energy conservation by S.&nbsp;aciditrophicus However, the absence of homologs for phosphate acetyltransferase and acetate kinase in the genome of S.&nbsp;aciditrophicus leaves it unclear as to how ATP is formed, as most fermentative bacteria rely on these two enzymes to synthesize ATP from acetyl coenzyme A (CoA) and phosphate. Here, we combine transcriptomic, proteomic, metabolite, and enzymatic approaches to show that S.&nbsp;aciditrophicus uses AMP-forming, acetyl-CoA synthetase (Acs1) for ATP synthesis from acetyl-CoA. acs1 mRNA and Acs1 were abundant in transcriptomes and proteomes, respectively, of S.&nbsp;aciditrophicus grown in pure culture and coculture. Cell extracts of S.&nbsp;aciditrophicus had low or undetectable acetate kinase and phosphate acetyltransferase activities but had high acetyl-CoA synthetase activity under all growth conditions tested. Both Acs1 purified from S.&nbsp;aciditrophicus and recombinantly produced Acs1 catalyzed ATP and acetate formation from acetyl-CoA, AMP, and pyrophosphate. High pyrophosphate levels and a high AMP-to-ATP ratio (5.9 ± 1.4) in S.&nbsp;aciditrophicus cells support the operation of Acs1 in the acetate-forming direction. Thus, S.&nbsp;aciditrophicus has a unique approach to conserve energy involving pyrophosphate, AMP, acetyl-CoA, and an AMP-forming, acetyl-CoA synthetase.ImportanceBacteria use two enzymes, phosphate acetyltransferase and acetate kinase, to make ATP from acetyl-CoA, while acetate-forming archaea use a single enzyme, an ADP-forming, acetyl-CoA synthetase, to synthesize ATP and acetate from acetyl-CoA. Syntrophus aciditrophicus apparently relies on a different approach to conserve energy during acetyl-CoA metabolism, as its genome does not have homologs to the genes for phosphate acetyltransferase and acetate kinase. Here, we show that S.&nbsp;aciditrophicus uses an alternative approach, an AMP-forming, acetyl-CoA synthetase, to make ATP from acetyl-CoA. AMP-forming, acetyl-CoA synthetases were previously thought to function only in the activation of acetate to acetyl-CoA