Documentation Reuse: Hot or Not? An Empirical Study

International audienceHaving available a high quality documentation is critical for software projects. This is why documentation tools such as Javadoc are so popular. As for code, documentation should be reused when possible to increase developer productivity and simplify maintenance. In this paper, we perform an empirical study of duplications in JavaDoc documentation on a corpus of seven famous Java APIs. Our results show that copy-pastes of JavaDoc documentation tags are abundant in our corpus. We also show that these copy-pastes are caused by four different kinds of relations in the underlying source code. In addition, we show that popular documentation tools do not provide any reuse mechanism to cope with these relations. Finally, we make a proposal for a simple but efficient automatic reuse mechanism

An Empirical Assessment of Bellon's Clone Benchmark

Context: Clone benchmarks are essential to the assessment and improvement of clone detection tools and algorithms. Among existing benchmarks, Bellon’s benchmark is widely used by the research community. However, a serious threat to the validity of this benchmark is that reference clones it contains have been manually validated by Bellon alone. Other persons may disagree with Bellon’s judgment. Ob-jective: In this paper, we perform an empirical assessment of Bellon’s benchmark. Method: We seek the opinion of eighteen participants on a subset of Bellon’s benchmark to determine if researchers should trust the reference clones it contains. Results: Our experiment shows that a significant amount of the reference clones are debatable, and this phe-nomenon can introduce noise in results obtained using this benchmark

Raters’ reliability in clone benchmarks construction

International audienceCloned code often complicates code maintenance and evolution and must therefore be effectively detected. One of the biggest challenges for clone detectors is to reduce the amount of irrelevant clones they found, called false positives. Several benchmarks of true and false positive clones have been introduced, enabling tool developers to compare, assess and fine-tune their tools. Manual inspection of clone candidates is performed by raters that do not have expertise on the underlying code. This way of building benchmarks might be unreliable when considering context-dependent clones i.e., clones valid for a specific purpose. Our goal is to investigate the reliability of rater judgments about context-dependent clones. We randomly select about 600 clones from two projects and ask several raters, including experts of the projects, to manually classify these clones. We observe that judgments of non expert raters are not always repeatable. We also observe that they seldomly agree with each others and with the expert. Finally, we find that the project and the fact that a clone is a true or false positive might have an influence on the agreement between the expert and non experts. Therefore, using non experts to produce clone benchmarks could be unreliable

Transit times and mean ages for nonautonomous and autonomous compartmental systems

We develop a theory for transit times and mean ages for nonautonomous compartmental systems. Using the McKendrick-von F\"orster equation, we show that the mean ages of mass in a compartmental system satisfy a linear nonautonomous ordinary differential equation that is exponentially stable. We then define a nonautonomous version of transit time as the mean age of mass leaving the compartmental system at a particular time and show that our nonautonomous theory generalises the autonomous case. We apply these results to study a nine-dimensional nonautonomous compartmental system modeling the terrestrial carbon cycle, which is a modification of the Carnegie-Ames-Stanford approach (CASA) model, and we demonstrate that the nonautonomous versions of transit time and mean age differ significantly from the autonomous quantities when calculated for that model

Near-complete elimination of mutant mtDNA by iterative or dynamic dose-controlled treatment with mtZFNs.

Mitochondrial diseases are frequently associated with mutations in mitochondrial DNA (mtDNA). In most cases, mutant and wild-type mtDNAs coexist, resulting in heteroplasmy. The selective elimination of mutant mtDNA, and consequent enrichment of wild-type mtDNA, can rescue pathological phenotypes in heteroplasmic cells. Use of the mitochondrially targeted zinc finger-nuclease (mtZFN) results in degradation of mutant mtDNA through site-specific DNA cleavage. Here, we describe a substantial enhancement of our previous mtZFN-based approaches to targeting mtDNA, allowing near-complete directional shifts of mtDNA heteroplasmy, either by iterative treatment or through finely controlled expression of mtZFN, which limits off-target catalysis and undesired mtDNA copy number depletion. To demonstrate the utility of this improved approach, we generated an isogenic distribution of heteroplasmic cells with variable mtDNA mutant level from the same parental source without clonal selection. Analysis of these populations demonstrated an altered metabolic signature in cells harbouring decreased levels of mutant m.8993T>G mtDNA, associated with neuropathy, ataxia, and retinitis pigmentosa (NARP). We conclude that mtZFN-based approaches offer means for mtDNA heteroplasmy manipulation in basic research, and may provide a strategy for therapeutic intervention in selected mitochondrial diseases.Medical Research Council, UK; EMBO Fellowship [ALTF 701-2013 to L.V.H.]; PhD fellowship from the Foundation for Science and Technology, Portugal through the GABBA Program, University of Porto (to P.R.G.); Experiments undertaken in the J-PC laboratory were supported by ANR Investissement d’Avenir [ANR-IIINSB-0014] and AFM [18566].This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/10.1093/nar/gkw67

Near-complete elimination of mutant mtDNA by iterative or dynamic dose-controlled treatment with mtZFNs

Mitochondrial diseases are frequently associated with mutations in mitochondrial DNA (mtDNA). In most cases, mutant and wild-type mtDNAs coexist, resulting in heteroplasmy. The selective elimination of mutant mtDNA, and consequent enrichment of wild-type mtDNA, can rescue pathological phenotypes in heteroplasmic cells. Use of the mitochondrially targeted zinc finger-nuclease (mtZFN) results in degradation of mutant mtDNA through site-specific DNA cleavage. Here, we describe a substantial enhancement of our previous mtZFN-based approaches to targeting mtDNA, allowing near-complete directional shifts of mtDNA heteroplasmy, either by iterative treatment or through finely controlled expression of mtZFN, which limits off-target catalysis and undesired mtDNA copy number depletion. To demonstrate the utility of this improved approach, we generated an isogenic distribution of heteroplasmic cells with variable mtDNA mutant level from the same parental source without clonal selection. Analysis of these populations demonstrated an altered metabolic signature in cells harbouring decreased levels of mutant m.8993T>G mtDNA, associated with neuropathy, ataxia, and retinitis pigmentosa (NARP). We conclude that mtZFN-based approaches offer means for mtDNA heteroplasmy manipulation in basic research, and may provide a strategy for therapeutic intervention in selected mitochondrial diseases

The Dementia Care Study (D-Care): Recruitment Strategies and Demographic Characteristics of Participants in a Pragmatic Randomized Trial of Dementia Care

INTRODUCTION: Pragmatic research studies that include diverse dyads of persons living with dementia (PLWD) and their family caregivers are rare. METHODS: Community-dwelling dyads were recruited for a pragmatic clinical trial evaluating three approaches to dementia care. Four clinical trial sites used shared and site-specific recruitment strategies to enroll health system patients. RESULTS: Electronic health record (EHR) queries of patients with a diagnosis of dementia and engagement of their clinicians were the main recruitment strategies. A total of 2176 dyads were enrolled, with 80% recruited after the onset of the pandemic. PLWD had a mean age of 80.6 years (SD 8.5), 58.4% were women, and 8.8% were Hispanic/Latino, and 11.9% were Black/African American. Caregivers were mostly children of the PLWD (46.5%) or spouses/partners (45.2%), 75.8% were women, 9.4% were Hispanic/Latino, and 11.6% were Black/African American. DISCUSSION: Health systems can successfully enroll diverse dyads in a pragmatic clinical trial

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Post Genome-Wide Association Studies of Novel Genes Associated with Type 2 Diabetes Show Gene-Gene Interaction and High Predictive Value

Recently, several Genome Wide Association (GWA) studies in populations of European descent have identified and validated novel single nucleotide polymorphisms (SNPs), highly associated with type 2 diabetes (T2D). Our aims were to validate these markers in other European and non-European populations, then to assess their combined effect in a large French study comparing T2D and normal glucose tolerant (NGT) individuals. rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24). With an area under the ROC curve of 0.86, only 15 novel loci were necessary to discriminate French individuals susceptible to develop T2D. strongly associate with T2D in French individuals, and mostly in populations of Central European descent but not in Moroccan subjects. Genes expressed in the pancreas interact together and their combined effect dramatically increases the risk for T2D, opening avenues for the development of genetic prediction tests

The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios