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opencc-zeroOct 2022View details →

Has long-distance flight ability been maintained by pigeons in highly insular habitats?

Aim: A reduction in dispersal ability has been thought to be a general trend for island land birds because of their physical isolation to a limited area, scarcity of predators, and ability to forage without flight in island habitats. However, recent studies have indicated that long-distance dispersal among island habitats may be maintained in island pigeon populations, which may be related to unstable food resource availability on a single island. Here, we investigated whether pigeons could maintain their long-distance dispersal ability to move among islands within the archipelago, even in highly insular conditions, by comparing two subspecies of Japanese wood pigeon (Columba janthina) distributed on islands with different levels of insularity. Location: The Ogasawara, Izu and Nansei Islands in the north-western Pacific Ocean Taxon: Japanese wood pigeon (Columba janthina) Methods: We compared morphological traits related to dispersal potential between the two subspecies: C. j. janthina and C. j. nitens. We performed phylogenetic and population genetic analyses based on genomic markers to indirectly assess dispersal ability via the rate of gene flow and determine how long C. j.nitens in a more insular habitat have been isolated for a long time. Results: C. j. nitens had a wing shape that was better suited for long-distance flight than that of C. j. janthina. Both subspecies maintained sufficient gene flow among the islands within their habitat archipelagos, with no evidence of isolation by distance. The divergence time of the two subspecies was 0.67 million years ago, which was sufficient to reduce dispersiveness compared to other cases of island land birds. Main conclusion: We showed that long-distance flight can be maintained under highly insular conditions despite long-term isolation from the ancestral populations. This indicates that the strategy of maintaining dispersal ability may also be possible in island systems, where organisms have repeatedly and globally shown reduced dispersal ability. Although further studies are required to reveal its evolutionary processes, our study provides an exceptional case for island birds' biogeography.

opencc-zeroMay 2024View details →

Data from: Small but connected islands can maintain populations and genetic diversity under climate change

In response to the striking effects of environmental change, conservation strategies often include the identification of conservation areas that can effectively maintain vulnerable species. Consequently, identifying system-specific conditions that maintain the demographic and genetic viability of species of conservation concern is essential. Connectivity plays a critical role in the persistence of populations. Islands have been model systems to understand connectivity and metapopulation processes and have emerged as particularly favorable targets for conservation. While islands can be isolated from mainland disturbances, it is unknown what degree of isolation is necessary to avoid unfavorable changes but remain sufficiently connected to maintain population viability. To test this question, we explored connectivity within the Apostle Islands, an archipelago of 22 islands within Lake Superior, by comparing historical and contemporary trends in ice bridge connectivity and by simulating the effect of reduced connectivity within this system. We developed a demographically informed individual-based model to explicitly test the role of connectivity to influence the persistence and genetic diversity of American marten (Martes americana), a forest carnivore at risk across its southern range boundary. We found that genetic diversity was resilient to moderate changes in ice cover, but a complete loss of connectivity resulted in rapid genetic erosion. Despite genetic erosion, populations persisted as long as nominal connectivity occurred between islands. Our work suggests that connectivity will decline, but martens would be resilient to moderate changes, and, in the short term, the Apostle Islands can act as a refuge along this species' southern range boundary. Identifying thresholds in connectivity that maintain populations but allow for isolation from disturbance will be necessary to identify suitable areas for species conservation across space and time.

opencc-zeroJun 2024View details →

Soil carbon maintained by perennial grasslands but lost in field crop systems over 30 years in a temperate Mollisol according to longitudinal, compaction-corrected, full-soil profile analysis

To mitigate climate change, some seek to store carbon from the atmosphere in agricultural soils. However, our understanding of how agriculture affects soil organic carbon (SOC) is muddied by studies 1) lacking longitudinal data, 2) ignoring bulk density changes, or 3) sampling only surface soils. To better understand SOC trends, here we measured changes over 30 years in density-corrected, full-soil-depth (90 cm) SOC stocks under 6 cropping systems and a restored prairie in a Mollisol of southern Wisconsin, USA. Cash-grain systems and alfalfa-based systems lost SOC. Prairie and rotationally-grazed pasture maintained SOC. Average SOC losses for cash-grain and alfalfa-based systems were -0.82 (±0.12) and -0.64 (±0.17) Mg C ha-1 yr-1, respectively. Sensitivity analysis showed that incomplete methodologies overestimated SOC improvements. Our findings using more comprehensive methods demonstrate the inadequacy of row-crop systems and the need for well-managed grasslands to protect SOC in productive agricultural soils of the Upper Midwest USA.

opencc-zeroJun 2024View details →

Polyandry and non-random fertilisation maintain long-term genetic diversity in an isolated island population of adders (Vipera berus)

Conservation genetic theory suggests that small and isolated populations should be subjected to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproductive adult population size of only 65 adult adders (range 12 to 171), the population has been able to maintain high levels of heterozygosity and allelic diversity similar to that observed in two mainland populations. Even a 14-year major "bottleneck" i.e., a reduction in adult adder numbers, encompassing at least four adder generations, did not result in any reduction in the island adders' heterozygosity and allelic diversity. Female adders are polyandrous, and fertilisation is non-random, which our empirical data and modelling suggest underpinning the island adders' ability to maintain a high level of heterozygosity. Our empirical results and subsequent modelling suggest that the positive genetic effects of polyandry in combination with non-random fertilisation, often overlooked in conservation genetic analyses, deserve greater consideration when predicting long-term survival of small and isolated populations.

opencc-by-4.0Jun 2024View details →

Ghost Echoes Revealed: Benchmarking Maintainability Metrics and Machine Learning Predictions Against Human Assessments

This repo contains a complete replication package, including raw data and scripts for the statistical analysis, for the paper "Ghost Echoes Revealed: Benchmarking Maintainability Metrics and Machine Learning Predictions Against Human Assessments" submitted to the industry track of the <a href="https://conf.researchr.org/home/icsme-2024" rel="nofollow">40th International Conference on Software Maintenance and Evolution (ICSME)</a>, Flagstaff, AZ, USA, Oct 6-11, 2024. <div> <h2>Authors</h2> <a href="https://github.com/codescene-research/maintainability-benchmarking-icsme-2024#authors"></a>Markus Borg, Marwa Ezzouhri, and Adam Tornhill</div> <div> <h2>Abstract</h2> <a href="https://github.com/codescene-research/maintainability-benchmarking-icsme-2024#abstract"></a>As generative AI is expected to increase global code volumes, the importance of maintainability from a human perspective will become even greater. Various methods have been developed to identify the most important maintainability issues, including aggregated metrics and advanced Machine Learning (ML) models. This study benchmarks several maintainability prediction approaches, including State-of-the-Art (SotA) ML, SonarQube's Maintainability Rating, CodeScene's Code Health, and Microsoft's Maintainability Index. Our results indicate that CodeScene matches the accuracy of SotA ML and outperforms the average human expert. Importantly, unlike SotA ML, CodeScene also provides end users with actionable code smell details to remedy identified issues. Finally, caution is advised with SonarQube due to its tendency to generate many false positives. Unfortunately, our findings call into question the validity of previous studies that solely relied on SonarQube output for establishing ground truth labels. To improve reliability in future maintainability and technical debt studies, we recommend employing more accurate metrics. Moreover, reevaluating previous findings with Code Health would mitigate this revealed validity threat.</div> <div> <h2>Repository Content</h2> Two Jupyter Notebooks.</div> <ul> <li> <ul> <li>uc1_maintainability_prediction.ipynb: A Notebook for Use Case 1 - Maintainability Prediction.</li> <li>uc2_liability_prediction.ipynb: A Notebook for Use Case 2 - Liability Prediction.</li> </ul> </li> <li>maintainability_data.csv: The dataset covering the 404 open-source files from the Maintainability Dataset (Bertrand et al., 2020) <ul> <li>Majority vote ground truth labels from Schnappinger et al. (2020)</li> <li>Low-level code metrics from Bertrand et al. (2023)</li> <li>Code Health</li> <li>SonarQube output, i.e., TD Ratio and TD Time</li> <li>Microsoft Maintainability index provided by <a href="https://plugins.jetbrains.com/plugin/13959-metricstree" rel="nofollow">MetricsTree</a></li> </ul> </li> </ul> <div> <h2>References</h2> </div> <ul> <li>Schnappinger et al., <a href="https://figshare.com/articles/dataset/A_Software_Maintainability_Dataset/12801215" rel="nofollow">A Software Maintainability Dataset</a>, 10.6084/m9.figshare.12801215, 2020.</li> <li>Schnappinger et al., Defining a Software Maintainability Dataset: Collecting, Aggregating and Analysing Expert Evaluations of Software Maintainability, in Proc. of the 36th International Conference on Software Maintenance and Evolution, pp. 278–289, 2020.</li> <li>S. Bertrand et al., Replication and Extension of Schnappinger’s Study on Human-level Ordinal Maintainability Prediction Based on Static Code Metrics, in Proc. of the 27th International Conference on Evaluation and Assessment in Software Engineering, pp. 241–246, 2023.</li> </ul>

opencc-by-4.0Jul 2024View details →

The Efficacy of Daily versus Weekly Ferrous Sulfate in Maintaining Normal Serum Ferritin Levels During Pregnancy: A Randomized Controlled Trial

Serum ferritin is the most reliable indication of stored iron in pregnancy, offering a noninvasive way to detect iron deficiency anemia before it occurs. Therefore, this study aimed to determine serum ferritin levels among women receiving daily versus weekly iron supplementation, with a secondary focus on comparing the proportion developing iron deficiency anemia and compli- ance rates between the two groups. Methods: This non-blinded randomized control trial involved non-anaemic pregnant women attend- ing antenatal clinics at two Teaching Hospitals in Osun State. One hundred twenty-five subjects were recruited to receive 65mg in the control group, while another 125 subjects in the active group re- ceived three tablets (195mg) of ferrous sulfate (Fesulf) once weekly for 17 weeks from the 20th to 37th weeks of gestation. The primary outcome measure was comparing mean serum ferritin levels in both groups at 37 weeks. Results: Among the 240 subjects analyzed, the 37-week serum ferritin level was higher in the daily group (73.26±26.67µg/L) compared to the weekly group (63.04±30.71 µg/L), p value=0.006. Four (3.36%) and 10 (8.26%) of our subjects had Iron deficiency anaemia. Nine subjects (3.75%) reported dyspepsia as a side effect. Daily 65 mg of Felsulf proved more effective than weekly 195mg in main- taining normal blood ferritin levels during pregnancy. Conclusions: Daily iron supplementation with 65mg ferrous sulfate was more effective at main- taining adequate maternal iron concentration in this group of non-anaemic pregnant women. This dosage is recommended for routine iron supplementation in our environment.

Fig. 8 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 8. Pseudogabucinia nisaeti sp. n. female. A – dorsal view, B – ventral view.

Fig. 5 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 5. Pseudalloptinus pithecophagae sp. n. female. A – dorsal view, B – ventral view.

Fig. 2 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 2. Hieracolichus philippinensis sp. n. female. A – dorsal view, B – ventral view.

Fig. 1 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 1. Hieracolichus philippinensis sp. n. male. A – dorsal view, B – ventral view.

Fig. 4 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 4. Pseudalloptinus pithecophagae sp. n. male. A – dorsal view, B – ventral view.

Fig. 7 in Captive individuals of endangered Philippine raptors maintain native feather mites (Acariformes: Pterolichoidea) species

Fig. 7. Pseudogabucinia nisaeti sp. n. male. A – dorsal view, B – ventral view.

opencc-by-4.0Sep 2018View details →

Response of E3 stage Radix balthica embryos maintained in contrasting temperatures and salinities for 24h

Sample datasets and video acquired using the EmbryoPhenomics platform. Experiment assessing influence of three (20, 25 and 30C) contrasting temperatures and two salinities (0 or 7 ppt) on the development of the aquatic gastropod Radix balthica. Exposure was initiated at the E3 developmental stage at which embryos are undergoing ciliary driven spinning. The EmbryoCV package was used to produce phenome-level data. Datasets and associated video for an individual embryo from each treatment (temperature and salinity combinations).

opencc-by-4.0Jan 2019View details →

The Delta Maintainability Model: Measuring Maintainability of Fine-Grained Code Changes Technical Report

Technical Report and dataset for "The Delta Maintainability Model: Measuring Maintainability of Fine-Grained Code Changes" submitted to the 2nd International Conference on Technical Debt (TechDebt 2019) - Montréal, Canada - May 26–27, 2019.

opencc-by-4.0Jun 2018View details →

Fig. 1 in The importance of isolated patches for maintaining local bird biodiversity and ecosystem function: a case study from the Pernambuco Center of Endemism, Northeast Brazil

Fig. 1. Rarefaction curve based at Mata do Cedro abundance and richness, state of Alagoas, Brazil.

opencc-by-4.0Jun 2018View details →

Fig. 2 in The importance of isolated patches for maintaining local bird biodiversity and ecosystem function: a case study from the Pernambuco Center of Endemism, Northeast Brazil

Fig. 2. Functional dendrogram of species of birds found at Mata do Cedro, state of Alagoas, Brazil.

opencc-zeroDec 2018View details →

Data from: Sexual signal loss in field crickets maintained despite strong sexual selection favoring singing males

Evolutionary biologists commonly seek explanations for how selection drives the emergence of novel traits. While trait loss is also predicted to occur frequently, few contemporary examples exist. In Hawaii, the Pacific field cricket (Teleogryllus oceanicus) is undergoing adaptive sexual signal loss due to natural selection imposed by eavesdropping parasitoids. Mutant male crickets ("flatwings") cannot sing. We measured the intensity of sexual selection on wing phenotype in a wild population. First, we surveyed the relative abundance of flatwings and "normal-wings" (non-mutants) on Oahu. Then, we bred wild-mated females' offspring to determine both female genotype with respect to the flatwing mutation and the proportion of flatwing males that sired their offspring. We found evidence of strong sexual selection favoring the production of song: females were predominantly homozygous normal-wing; their offspring were sired disproportionately by singing males; and at the population level, flatwing males became less common following a single sexual selection event. We report a selection coefficient describing the total (pre- and postcopulatory) sexual selection favoring normal-wing males in nature. Given the maintenance of the flatwing phenotype in Hawaii in recent years, this substantial sexual selection additionally suggests an approximate strength of opposing natural selection that favors silent males.

opencc-by-4.0Dec 2021View details →

Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

1. spaSPT data for endogenously tagging HaloTag-YY1 in mESCs (clones YN11 and YN31). 2. spaSPT data for HaloTag-YY1 in CTCF- (clone CD1) or RAD21- (clone RD35) depleted mESCs. 3. sptSPT data for stably expressing HaloTag-YY1 in clone PBYN2 and YY1-HaloTag in clone PBYC3.   <div> </div>

opencc-zeroJul 2021View details →

Win some, lose some: mesocosm communities maintain community productivity despite lower phosphorus availability because of increased species diversity

Aims The restoration of degraded ecosystems typically focuses on establishing assemblages of target species, but successful recovery should also be evaluated by the ecosystem's functioning to guarantee long-term persistence. We investigated how the processes underlying community assembly (i.e. species loss, species gain and changes in abundance of resident species) influenced ecosystem functioning in experimental grassland communities in different restoration states. Location A greenhouse experiment in Northern Flanders, Belgium. Methods We set up a mesocosm experiment with communities of nineteen planted species, ranging from slow-growing species from poorly productive Nardus grasslands to fast-growing species from highly productive Lolium perenne grasslands. We categorized the mesocosms into different grassland restoration states based on known abiotic and biotic restoration barriers for semi-natural grassland restoration: soil phosphorus levels and soil biota communities. After two growing seasons, we used the CAFE approach, an ecological application of the Price equation, to partition the effects of plant community assembly on ecosystem functioning (here community productivity) for the different restoration states. Results Adding soil biota communities sampled from reference Nardus grasslands versus more intensively managed grasslands did not have a significant effect on either plant species richness or biomass productivity. Lower soil phosphorus concentrations (i.e. abiotic restoration) resulted in a higher plant species richness. However, the net effect on productivity was close to zero. The increase in productivity caused by species gains was compensated through decreases in productivity caused by species loss and by decreases in the abundance or functioning of species that are present in both abiotically degraded and abiotically restored states. Conclusions Not only species richness but also species identity resulted in changes in ecosystem functioning (i.e. productivity), even though the net functional effects were close to zero. More specifically, we found that species richness-driven increases in productivity were counterbalanced by resource-driven and species identity-driven reductions in productivity.