Are 20% of files responsible for 80% of defects?

Background: Over the past two decades a mixture of anecdote from the industry and empirical studies from academia have suggested that the 80:20 rule (otherwise known as the Pareto Principle) applies to the relationship between source code files and the number of defects in the system: a small minority of files (roughly 20%) are responsible for a majority of defects (roughly 80%). Aims: This paper aims to establish how widespread the phenomenon is by analysing 100 systems (previous studies have focussed on between one and three systems), with the goal of whether and under what circumstances this relationship does hold, and whether the key files can be readily identified from basic metrics. Method: We devised a search criterion to identify defect fixes from commit messages and used this to analyse 100 active Github repositories, spanning a variety of languages and domains. We then studied the relationship between files, basic metrics (churn and LOC), and defect fixes. Results: We found that the Pareto principle does hold, but only if defects that incur fixes to multiple files count as multiple defects. When we investigated multi-file fixes, we found that key files (belonging to the top 20%) are commonly fixed alongside other much less frequently-fixed files. We found LOC to be poorly correlated with defect proneness, Code Churn was a more reliable indicator, but only for extremely high values of Churn. Conclusions: It is difficult to reliably identify the "most fixed" 20% of files from basic metrics. However, even if they could be reliably predicted, focussing on them would probably be misguided. Although fixes will naturally involve files that are often involved in other fixes too, they also tend to include other less frequently-fixed files

Mining State-Based Models from Proof Corpora

Interactive theorem provers have been used extensively to reason about various software/hardware systems and mathematical theorems. The key challenge when using an interactive prover is finding a suitable sequence of proof steps that will lead to a successful proof requires a significant amount of human intervention. This paper presents an automated technique that takes as input examples of successful proofs and infers an Extended Finite State Machine as output. This can in turn be used to generate proofs of new conjectures. Our preliminary experiments show that the inferred models are generally accurate (contain few false-positive sequences) and that representing existing proofs in such a way can be very useful when guiding new ones.Comment: To Appear at Conferences on Intelligent Computer Mathematics 201

Structural and mechanistic mapping of a unique fumarate reductase

The 1.8 Å resolution crystal structure of the tetraheme flavocytochrome c3, Fcc3, provides the first mechanistic insight into respiratory fumarate reductases or succinate dehydrogenases. The multi-redox center, three-domain protein shows a 40 Å long ‘molecular wire’ allowing rapid conduction of electrons through a new type of cytochrome domain onto the active site flavin, driving the reduction of fumarate to succinate. In this structure a malate-like molecule is trapped in the enzyme active site. The interactions between this molecule and the enzyme suggest a clear mechanism for fumarate reduction in which the substrate is polarized and twisted, facilitating hydride transfer from the reduced flavin and subsequent proton transfer. The enzyme active site in the oxidized form is completely buried at the interface between the flavin-binding and the clamp domains. Movement of the cytochrome and clamp domains is postulated to allow release of the product

Satisfaction with the Use of Different Technologies for Insulin Delivery and Glucose Monitoring Among Adults with Long-Standing Type 1 Diabetes and Problematic Hypoglycemia: 2-Year Follow-Up in the HypoCOMPaSS Randomized Clinical Trial

Background In the HypoCOMPaSS trial, adults with long-standing type 1 diabetes and problematic hypoglycaemia were randomised to compare insulin pump (CSII) vs multiple daily injections (MDI) and real-time continuous glucose monitoring (RT-CGM) vs conventional self-monitoring (SMBG). Our aim was to investigate participants\u27 satisfaction with these technologies at 6-month RCT endpoint and at 2-year follow-up. Methods Participants completed the Insulin Treatment Satisfaction Questionnaire (ITSQ) subscales \u27device delivery\u27 and \u27hypoglycaemia control\u27; and Glucose Monitoring Experience Questionnaire (GME-Q), assessing \u27convenience\u27, \u27effectiveness\u27, \u27intrusiveness\u27 and \u27total satisfaction\u27. We assessed change over time and between group differences by insulin and monitoring modalities. Results Participants (N=96) were: 64% women, aged 49\ub112 years, diabetes duration 29\ub112 years. At 6 months, participants reported improvements compared to baseline (all p<0.001) in satisfaction with insulin \u27delivery device\u27 (r=0.39) and \u27hypoglycaemia control\u27 (r=0.52), and trends towards significance in perceived \u27effectiveness\u27 (r=0.42) and \u27intrusiveness\u27 (r=0.27) of monitoring device (but not \u27convenience\u27, p=0.139). All improvements were sustained at 2 years. At 6 months, the only difference between arms was that greater satisfaction with insulin \u27delivery device\u27 was reported in the CSII group compared to MDI (p<0.001, r=0.40). No between-group differences were observed at 2 years. Conclusions Overall, significant improvements in participant satisfaction with diabetes technologies were observed over the 6-month RCT, in all domains except \u27convenience\u27, maintained at 2 years. While HypoCOMPaSS demonstrated non-inferiority of SMBG versus CGM, and MDI versus CSII in terms of biomedical outcomes, detailed assessments confirm participants\u27 satisfaction with delivery device was greater in those allocated to CSII than MDI

Unsupervised home use of an overnight closed-loop system over 3-4 weeks: a pooled analysis of randomized controlled studies in adults and adolescents with type 1 diabetes.

AIMS: To compare overnight closed-loop and sensor-augmented pump therapy in patients with type 1 diabetes by combining data collected during free-living unsupervised randomized crossover home studies. METHODS: A total of 40 participants with type 1 diabetes, of whom 24 were adults [mean ± standard deviation (s.d.) age 43 ± 12 years and glycated haemoglobin (HbA1c) 8.0 ± 0.9%] and 16 were adolescents (mean ± s.d. age 15.6 ± 3.6 years and HbA1c 8.1 ± 0.8%), underwent two periods of sensor-augmented pump therapy in the home setting, in combination with or without an overnight closed-loop insulin delivery system that uses a model predictive control algorithm to direct insulin delivery. The order of the two interventions was random; each period lasted 4 weeks in adults and 3 weeks in adolescents. The primary outcome was time during which sensor glucose readings were in the target range of 3.9-8.0 mmol/l. RESULTS: The proportion of time when sensor glucose was in the target range (3.9-8.0 mmol/l) overnight (between 24:00 and 08:00 hours) was 18.5% greater during closed-loop insulin delivery than during sensor-augmented therapy (p < 0.001). Closed-loop therapy significantly reduced mean overnight glucose levels by 0.9 mmol/l (p < 0.001), with no difference in glycaemic variability, as measured by the standard deviation of sensor glucose. Time spent above the target range was reduced (p = 0.001), as was time spent in hypoglycaemia (<3.9 mmol/l; p = 0.014) during closed-loop therapy. Lower mean overnight glucose levels during closed-loop therapy were brought about by increased overnight insulin delivery (p < 0.001) without changes to the total daily delivery (p = 0.84). CONCLUSION: Overnight closed-loop insulin therapy at home in adults and adolescents with type 1 diabetes is feasible, showing improvements in glucose control and reducing the risk of nocturnal hypoglycaemia.Juvenile Diabetes Research Foundation (#22-2009-802) and Diabetes UK (BDA07/0003549) with additional support for the Artificial Pancreas work by National Institute of Diabetes and Digestive and Kidney Diseases (1R01DK085621), and National Institute for Health Research Cambridge Biomedical Research Centre. Abbott Diabetes Care supplied continuous glucose delivery devices and sensors and modified devices to facilitate real-time connectivity.This if the final version of the article. It was originally published by Wiley in Diabetes, Obesity and Metabolism at http://onlinelibrary.wiley.com/doi/10.1111/dom.12427/abstrac

The unusual kinetics of lactate dehydrogenase of Schistosoma mansoni and their role in the rapid metabolic switch after penetration of the mammalian host

Lactate dehydrogenase (LDH) from Schistosoma mansoni has peculiar properties for a eukaryotic LDH. Schistosomal LDH (SmLDH) isolated from schistosomes, and the recombinantly expressed protein, are strongly inhibited by ATP, which is neutralized by fructose-1,6-bisphosphate (FBP). In the conserved FBP/anion binding site we identified two residues in SmLDH (Val187 and Tyr190) that differ from the conserved residues in LDHs of other eukaryotes, but are identical to conserved residues in FBP-sensitive prokaryotic LDHs. Three-dimensional (3D) models were generated to compare the structure of SmLDH with other LDHs. These models indicated that residues Val187, and especially Tyr190, play a crucial role in the interaction of FBP with the anion pocket of SmLDH. These 3D models of SmLDH are also consistent with a competitive model of SmLDH inhibition in which ATP (inhibitor) and FBP (activator) compete for binding in a well-defined anion pocket. The model of bound ATP predicts a distortion of the nearby key catalytic residue His195, resulting in enzyme inhibition. To investigate a possible physiological role of this allosteric regulation of LDH in schistosomes we made a kinetic model in which the allosteric regulation of the glycolytic enzymes can be varied. The model showed that inhibition of LDH by ATP prevents fermentation to lactate in the free-living stages in water and ensures complete oxidation via the Krebs cycle of the endogenous glycogen reserves. This mechanism of allosteric inhibition by ATP prevents the untimely depletion of these glycogen reserves, the only fuel of the free-living cercariae. Neutralization by FBP of this ATP inhibition of LDH prevents accumulation of glycolytic intermediates when S. mansoni schistosomula are confronted with the sudden large increase in glucose availability upon penetration of the final host. It appears that the LDH of S. mansoni is special and well suited to deal with the variations in glucose availability the parasite encounters during its life cycle.</p

Restoration of self-awareness of hypoglycemia in adults with long-standing type 1 diabetes: hyperinsulinemic-hypoglycemic clamp substudy results from the HypoCOMPaSS trial.

OBJECTIVE: Impaired awareness of hypoglycemia (IAH) and defective counterregulation significantly increase severe hypoglycemia risk in type 1 diabetes (T1D). We evaluated restoration of IAH/defective counterregulation by a treatment strategy targeted at hypoglycemia avoidance in adults with T1D with IAH (Gold score ≥4) participating in the U.K.-based multicenter HypoCOMPaSS randomized controlled trial. RESEARCH DESIGN AND METHODS: Eighteen subjects with T1D and IAH (mean ± SD age 50 ± 9 years, T1D duration 35 ± 10 years, HbA1c 8.1 ± 1.0% [65 ± 10.9 mmol/mol]) underwent stepped hyperinsulinemic-hypoglycemic clamp studies before and after a 6-month intervention. The intervention comprised the HypoCOMPaSS education tool in all and randomized allocation, in a 2 × 2 factorial study design, to multiple daily insulin analog injections or continuous subcutaneous insulin infusion therapy and conventional glucose monitoring or real-time continuous glucose monitoring. Symptoms, cognitive function, and counterregulatory hormones were measured at each glucose plateau (5.0, 3.8, 3.4, 2.8, and 2.4 mmol/L), with each step lasting 40 min with subjects kept blinded to their actual glucose value throughout clamp studies. RESULTS: After intervention, glucose concentrations at which subjects first felt hypoglycemic increased (mean ± SE from 2.6 ± 0.1 to 3.1 ± 0.2 mmol/L, P = 0.02), and symptom and plasma metanephrine responses to hypoglycemia were higher (median area under curve for symptoms, 580 [interquartile range {IQR} 420-780] vs. 710 [460-1,260], P = 0.02; metanephrine, 2,412 [-3,026 to 7,279] vs. 5,180 [-771 to 11,513], P = 0.01). Glycemic threshold for deterioration of cognitive function measured by four-choice reaction time was unchanged, while the color-word Stroop test showed a degree of adaptation. CONCLUSIONS: Even in long-standing T1D, IAH and defective counterregulation may be improved by a clinical strategy aimed at hypoglycemia avoidance

Cyclophilin40 isomerase activity is regulated by a temperature-dependent allosteric interaction with Hsp90

Cyclophilin 40 (Cyp40) comprises an N-terminal cyclophilin domain with peptidyl-prolyl isomerase (PPIase) activity and a C-terminal tetratricopeptide repeat (TPR) domain that binds to the C-terminal–EEVD sequence common to both heat shock protein 70 (Hsp70) and Hsp90. We show in the present study that binding of peptides containing the MEEVD motif reduces the PPIase activity by ∼30%. CD and fluorescence assays show that the TPR domain is less stable than the cyclophilin domain and is stabilized by peptide binding. Isothermal titration calorimetry (ITC) shows that the affinity for the–MEEVD peptide is temperature sensitive in the physiological temperature range. Results from these biophysical studies fit with the MD simulations of the apo and holo (peptide-bound) structures which show a significant reduction in root mean square (RMS) fluctuation in both TPR and cyclophilin domains when–MEEVD is bound. The MD simulations of the apo-protein also highlight strong anti-correlated motions between residues around the PPIase-active site and a band of residues running across four of the seven helices in the TPR domain. Peptide binding leads to a distortion in the shape of the active site and a significant reduction in these strongly anti-correlated motions, providing an explanation for the allosteric effect of ligand binding and loss of PPIase activity. Together the experimental and MD results suggest that on heat shock, dissociation of Cyp40 from complexes mediated by the TPR domain leads to an increased pool of free Cyp40 capable of acting as an isomerase/chaperone in conditions of cellular stress

Accuracy of Continuous Glucose Monitoring During Three Closed-Loop Home Studies Under Free-Living Conditions.

OBJECTIVES: Closed-loop (CL) systems modulate insulin delivery based on glucose levels measured by a continuous glucose monitor (CGM). Accuracy of the CGM affects CL performance and safety. We evaluated the accuracy of the Freestyle Navigator(®) II CGM (Abbott Diabetes Care, Alameda, CA) during three unsupervised, randomized, open-label, crossover home CL studies. MATERIALS AND METHODS: Paired CGM and capillary glucose values (10,597 pairs) were collected from 57 participants with type 1 diabetes (41 adults [mean±SD age, 39±12 years; mean±SD hemoglobin A1c, 7.9±0.8%] recruited at five centers and 16 adolescents [mean±SD age, 15.6±3.6 years; mean±SD hemoglobin A1c, 8.1±0.8%] recruited at two centers). Numerical accuracy was assessed by absolute relative difference (ARD) and International Organization for Standardization (ISO) 15197:2013 15/15% limits, and clinical accuracy was assessed by Clarke error grid analysis. RESULTS: Total duration of sensor use was 2,002 days (48,052 h). Overall sensor accuracy for the capillary glucose range (1.1-27.8 mmol/L) showed mean±SD and median (interquartile range) ARD of 14.2±15.5% and 10.0% (4.5%, 18.4%), respectively. Lowest mean ARD was observed in the hyperglycemic range (9.8±8.8%). Over 95% of pairs were in combined Clarke error grid Zones A and B (A, 80.1%, B, 16.2%). Overall, 70.0% of the sensor readings satisfied ISO criteria. Mean ARD was consistent (12.3%; 95% of the values fall within ±3.7%) and not different between participants (P=0.06) within the euglycemic and hyperglycemic range, when CL is actively modulating insulin delivery. CONCLUSIONS: Consistent accuracy of the CGM within the euglycemic-hyperglycemic range using the Freestyle Navigator II was observed and supports its use in home CL studies. Our results may contribute toward establishing normative CGM performance criteria for unsupervised home use of CL.Juvenile Diabetes Research Foundation (#22-2009-802), Diabetes UK (BDA07/0003549) and Seventh Framework Programme of the European Union (Grant Agreement number 247138) with additional support for the Artificial Pancreas work by National Institute of Diabetes and Digestive and Kidney Diseases (1R01DK085621), Wellcome Strategic Award (100574/Z/12/Z), and National Institute for Health Research Cambridge Biomedical Research Centre.This is the final version of the article. It first appeared from Mary Ann Liebert via http://dx.doi.org/10.1089/dia.2015.006

Home use of closed loop insulin delivery improves overnight glucose control in adults with type 1 diabetes: A four-week multicentre randomised crossover study

This is the author accepted manuscript and will be embargoed until 16/12/14. The final published version can be found here: http://www.thelancet.com/journals/landia/article/PIIS2213-8587(14)70114-7/fulltext#article_upsell.Background: We assessed whether overnight home use of automated closed loop insulin delivery (artificial pancreas) improves glucose control. Methods: We studied 24 adults with type 1 diabetes in a multicentre crossover study design comparing four weeks of overnight closed loop using a model predictive control algorithm to direct insulin delivery, with four weeks of insulin pump therapy in which participants used real-time display of continuous glucose monitoring independent of their pumps as control. Primary outcome was time when glucose was in the target range of 3•9 and 8•0mmol/l between midnight to 07:00. Analyses were by intention to treat. Trial registration ClinicalTrials.gov NCT01440140. Findings: Closed loop was utilised over median 8•3 (interquartile range 6•0, 9•6)hours on 555nights (86%). Proportion of time when overnight glucose was in target range was significantly higher during closed loop compared to control by 13•5% (95% CI, 7•3-19•7; p<0•001). Mean overnight glucose (8•2±0•9 vs. 9•0±1•3mmol/l; p=0•005) and time spent above target (44•3%±11•9 vs. 57•1%±15•6; p=0•001) were significantly lower during closed loop. Time spent below target was low and comparable [1•8%( 0•6, 3•6) vs. 2•1%(0•7, 3•9);p=0•28]. Lower mean overnight glucose was brought about by increased overnight insulin delivery [6•4 (4•5, 8•1) vs. 4•9 (3•7, 6•3)units;p<0•001) without changing the total daily insulin amount [34•5 (29•3, 48•4) vs. 35•4 (29•7, 45•2)units;p=0•32]. No severe hypoglycaemia episodes occurred during control period and two during closed loop not related to algorithm instructions. Interpretation: Unsupervised overnight closed loop at home is feasible and may improve glucose control in adults with type 1 diabetes