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opencc-by-4.0Aug 2021View details →

Contrasting Third-Party Package Management User Experience

The management of third-party package dependencies is crucial to most technology stacks, with package managers acting as brokers to ensure that a verified package is correctly installed, configured, or removed from an application. Diversity in technology stacks has led to dozens of package ecosystems with their own management features. While recent studies have shown that developers struggle to migrate their dependencies, the common assumption is that package ecosystems are used without any issue.  In this study, we explore 13 package ecosystems to understand whether their features correlate with the experience of their users. By studying experience through the questions that developers ask on the question-and-answer site Stack Overflow, we find that developer questions are  grouped into three themes (i.e., Package management, Input-Output, and Package Usage). Our preliminary analysis indicates that specific features are correlated with the user experience. Our work lays out future directions to investigate the trade-offs involved in designing the ideal package ecosystem.

opencc-by-4.0Jun 2007View details →

Figure 3 in Deforestation affects biogeographical regionalization: a case study contrasting potential and extant distributions of Mexican terrestrial mammals

Figure 3. Mexican regionalization based on consensus cladogram of t1.

opencc-zeroAug 2021View details →

Phase-contrast MRI data of 18 Chiari-I malformation patients and 21 controls

We collected phase-contrast MRI data (5-mm midline sagittal section, rostro-caudal direction) and obtained average velocity in certain Regions-0f-Interest (ROIs). The measured ROIs are cerebellar tonsil, ventral spinal subarachnoid space, dorsal spinal subarachnoid space, upper portion of syrinxes, upper cervical cord, and medulla. Data obtained from 18 Chiari-I patients (preoperative and postoperative) and 21 controls are included. Because the preoperative MRI data was missing in one patient, the preoperative studies included 17 MRI sessions. The unit of the data is cm/sec. The data are synchronized with pre-processing so that the rise of the caudal CSF movement be placed at the center of the cardiac cycle.

opencc-by-nd-4.0Jun 2010View details →

FIGURE 3 in Contrasted Ecological Repartition Of The Northern Fowl Mite Ornithonyssus Sylviarum (Mesostigmata: Macronyssidae) And The Chicken Red Mite Dermanyssus Gallinae (Mesostigmata: Dermanyssidae)

FIGURE 3: COI-based phylogenetic topologie involving all haplotypes isolated in Roy et al. (2009b), plus sequences newly obtained from French and North American Ornithonyssus sylviarum and from North American Dermanyssus individuals. Maximum-likelihood (PHYML). Numbers at nodes represent aLRT values.

opencc-by-nd-4.0Jun 2010View details →

FIGURE 2 in Contrasted Ecological Repartition Of The Northern Fowl Mite Ornithonyssus Sylviarum (Mesostigmata: Macronyssidae) And The Chicken Red Mite Dermanyssus Gallinae (Mesostigmata: Dermanyssidae)

FIGURE 2: Percentage of samples containing identified hematophagous mites, according to the type of environment. Solid bar: wild avifauna (n=166), grey bar: industrial fowl (layer and chicken farms) (n=132), open bar: other domestic birds (n=12).

opencc-by-nd-4.0Jun 2010View details →

FIGURE 1 in Contrasted Ecological Repartition Of The Northern Fowl Mite Ornithonyssus Sylviarum (Mesostigmata: Macronyssidae) And The Chicken Red Mite Dermanyssus Gallinae (Mesostigmata: Dermanyssidae)

FIGURE 1: Location of samples collected in France and containing either Dermanyssus. gallinae s. str. (ie non L1) (solid dots) or Ornithonissus sylviarum (open dots). The shape of dots represents environmental information: circle for industrial fowls, triangle for amateur fowl houses, trapezoid for pet bird breeding facilities, square for game bird breeding facilities, 5-branch star for wild avifauna not sampled in orchard/field agroecosystems, 8-branch star for wild avifauna sampled in orchard/field agroecosystems. IF industrial fowl farms, AF amateur breeding facilities, fowl, PB amateur breeding facilities, pet birds, BG amateur breeding facilities, game birds, WA wild avifauna sampled in orchard or field agroecosystems, WNA, wild avifauna not sampled in orchard or field agroecosystem.

Figure 16. Hemiphlebia mirabilis Selys, 1869 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)

Figure 16. Hemiphlebia mirabilis Selys, 1869, anterior view of head.

Figure 15. Hemiphlebia mirabilis Selys, 1869 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)

Figure 15. Hemiphlebia mirabilis Selys, 1869, dorsal view of head.

Figure 8 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)

Figure 8. Electrohemiphlebia barucheli gen. et sp. nov., holotype ARC 372.1, left view of thorax.

Figure 5 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)

Figure 5. Electrohemiphlebia barucheli gen. et sp. nov., holotype ARC 372.1, dorsal view of head.

Figure 17. Hemiphlebia mirabilis Selys, 1869 in Phase contrast X-ray synchrotron microtomography and the oldest damselflies in amber (Odonata: Zygoptera: Hemiphlebiidae)

Figure 17. Hemiphlebia mirabilis Selys, 1869, ventral view of fore tibia.

opencc-zeroOct 2021View details →

Exploring changes in ecosystem service values in strongly human-impacted, contrasting agro-ecological environments

Evaluating the impacts of land-use/land-cover (LULC) changes on ecosystem service values (ESVs) is essential for sustainable use and management of ecosystems. In this study, we evaluated the impact of LULC changes on ESVs over the period 1982–2016/17 in contrasting, strongly human-impacted agro-ecological environments: Guder (highland), Aba Gerima (midland), and Debatie (lowland) watersheds of the Upper Blue Nile basin, Ethiopia. During the study period, the continuous expansion of cultivated land at the expense of natural vegetation (bushland, forest, and grazing land) severely reduced the total ESV by about US$58 thousand (35%) in Aba Gerima and US$31 thousand (29%) in Debatie watersheds. In contrast, the unprecedented expansion of plantations, mainly through the planting of Acacia decurrens, helped the total ESV rebound by about US$71 thousand (54%) in Guder watershed after 2006, after it had decreased by about US$61 thousand (32%) between 1982 and 2006. The reduction in natural forest area was the major contributor to the loss of total ESV in the study watersheds, ranging from a reduction of US$31 thousand (63%) in Debatie to US$96.9 thousand (70%) in Guder between 1982 and 2016/17. On an area-specific basis, LULC changes reduced the average ESV from US$560 ha–1 yr–1 (1982) in Guder to US$306 ha–1 yr–1 (2017) in Debatie watersheds. Specific ESVs such as provisioning (mainly as food production) and regulating services (mainly as erosion control and climate regulation) accounted for most of the total ESVs estimated for the study watersheds. In most cases the total and specific ESVs of the watersheds were negatively associated with the population growth, which in turn was positively associated with the expansion of cultivated land over the study period. In Guder watershed, however, ESVs were positively associated with population growth, especially after 2012. This resulted primarily from the conversion of cultivated land to plantations (predominantly with nitrogen-fixing Acacia decurrens trees) because of the farmers' growing desire to rehabilitate degraded cultivated land while simultaneously generating income through the sale of charcoal from this fast-growing tree. Our results suggest, therefore, that future policy measures and directions should focus on improving vegetation cover through planting multipurpose trees such as Acacia decurrens to prevent future loss of ESV in the midland and lowland regions of the Upper Blue Nile basin and beyond.

opencc-by-4.0Oct 2024View details →

Phase-contrast time-lapses of seven bacterial species growing in microfluidic mother machine traps

This dataset and software accompany the article "Rapid label-free identification of seven bacterial species using microfluidics, single-cell time-lapse phase-contrast microscopy, and deep learning-based image and video classification" for reproducing the results. In the study, deep-learning models are trained to classify phase-contrast videos (time-lapses) of bacteria growing in microfluidic chip traps. The dataset consists of lab isolates of the species Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Enterococcus faecalis, Proteus mirabilis, and Staphylococcus aureus. The video clips have around 30 frames each, captured during one hour of growth (2 minutes between each frame). The whole dataset consists of around 620,000 images from 19,500 traps. Additionally, the package contains software to re-run the experiments, generate output metrics, and build the graphs in the article.

opencc-zeroOct 2022View details →

Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies

Aim: Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow. Taxon: Dascyllus marginatus (endemic) and Dascyllus abudafur (widespread). Location: Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. Methods: We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. Results: Dascyllus marginatus inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. Dascyllus abudafur species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of D. marginatus had an order of magnitude higher genetic differentiation compared to D. abudafur, as well as several outlier loci (suggesting selective pressure), which were absent in D. abudafur despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. Main conclusions: The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.

opencc-zeroOct 2022View details →

Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the Erinaceus hedgehogs species complex, offering a unique comparison of two secondary contact zones between Erinaceus europaeus and E. roumanicus. Results confirmed diversification of the genus during the Pleistocene period and detected a new refugial lineage of E. roumanicus outside the Mediterranean region, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from E. europaeus to E. roumanicus suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different ages and thus of the different stages of evolution of reproductive isolating mechanisms in each hybrid zone.

opencc-zeroNov 2022View details →

Contrasting soil- and canopy-nurse effects on dependent species in metalliferous systems may be explained by dominant plant functional strategies

Plant-plant interaction studies in metalliferous systems have focused either on the role of facilitation or on the negative effects of elemental allelopathy. However, no studies have investigated both of these effects in the same system, and their relationships with the functional strategy of the nurse species, although this is crucial for the ecological restoration of polluted sites. We assessed the effects of two dominant nurse species, with apparent contrasting strategies, on two target species on a slag heap in the Pyrenees (France). We quantified both long-term soil-engineering and short-term canopy effects on the growth of two target species. We also measured morphological traits and leaf metal concentration of the two nurse species and their effects on air moisture, temperature, and vapour pressure deficit. Nurse functional strategies, as inferred from morphological traits and leaf metal concentration seem to drive their long-term soil engineering effects on target species: Gypsophila repens, the relatively larger and more exploitative species with high leaf metal concentration, had negative long-term effects likely due to elemental allelopathy, whereas Minuartia verna, the relatively smaller and more conservative species with a lower amount of metals in leaves, had neutral long-term effects. Although Gypsophila repens had a slightly stronger positive effect on microclimate than Minuartia verna, this did not turn into higher short-term effects for the target species. Our study highlights the possible role of the nurse's functional strategies in driving the relative importance of long and short-term effects on target species in metalliferous systems. This knowledge is key to increasing our understanding of plant-plant interaction outcomes in metalliferous systems and our ability to restore polluted environments.

opencc-zeroNov 2022View details →

Higher-order sequences of vocal mimicry performed by male Albert's lyrebirds are socially transmitted and enhance acoustic contrast

Most studies of acoustic communication focus on short units of vocalisation such as songs, yet these units are often hierarchically organised into higher-order sequences, and outside human language, little is known about the drivers of sequence structure. Here we investigate the organisation, transmission, and function of vocal sequences sung by male Albert's lyrebirds (Menura alberti), a species renowned for vocal imitations of other species. We quantified the organisation of mimetic units into sequences and examined the extent to which these sequences are repeated within and between individuals and shared among populations. We found that individual males organised their mimetic units into stereotyped sequences. Sequence structures were shared within and to a lesser extent among populations, implying that sequences were socially transmitted. Across the entire species range, mimetic units were sung with immediate variety and a high acoustic contrast between consecutive units, suggesting that sequence structure is a means to enhance receiver perceptions of repertoire complexity. Our results provide evidence that higher-order sequences of vocalisations can be socially transmitted, and that the order of vocal units can be functionally significant. We conclude that, to fully understand vocal behaviours, we must study both the individual vocal units and their higher-order temporal organisation.

opencc-by-4.0Nov 2022View details →

Improving magnetic STEM-differential phase contrast imaging using precession

Scanning transmission electron microscopy datasets and processing files used in the journal publication "Improving Magnetic STEM-Differential Phase Contrast Imaging using Precession". DOI link to publication: <a href="https://doi.org/10.1093/micmic/ozad001">https://doi.org/10.1093/micmic/ozad001</a>   Prerequisites To run the scripts necessary to process the files, the open source packages JupyterLab, HyperSpy, pyXem, and fpd need to be installed. These notebooks were created with these package versions: <ul> <li>hyperspy 1.6.4</li> <li>pyxem 0.13.3</li> <li>fpd 0.2.0</li> <li>jupyterlab 3.2.0</li> </ul>   Data files and processing scripts Data files are collected in .zip folders and have names that start with "d00..", while processing scripts are in the Jupyter Notebook .ipynb data format whose names start with "p00..". These files are divided into three main processing steps, outlined as follows: <ol> <li>Processing of raw data: Raw data files can be found in the d001_scans.zip folder. These are processed with the p002_get_dpc_raw.ipynb script which uses either the center of mass or phase correlation methods.</li> <li>D-scan correction: The processed files from the previous step are saved in the d002_dpc_raw.zip folder. The p003_get_dpc_cor.ipynb script performs a d-scan correction on these files and saves the output in the d003_dpc_cor.zip folder. <ul> <li>Virtual segmented detector algorithm: For comparison purposes to the other processing algorithms, a virtual segmented detector algorithm was developed and can be found in the p004_segmented_detector.ipynb script. This algorithm extracts a linear d-scan plane from already processed phase correlation files found in d002_dpc_raw.zip, subtracts it from the raw data files found in d001_scans.zip, and finally performs the processing algorithm.</li> </ul> </li> <li>Plotting files: The p005_plot_dpc_images.ipynb script creates the figures as seen in the journal publication. The input files are those found in d003_dpc_cor.zip from the previous processing step.</li> </ol>

opencc-zeroNov 2022View details →

Contrasting intra-annual population dynamics of two codominant species are consistent across spatial and temporal scales

1. Despite asymmetric competition and a wide array of functional similarities, two ecologically important C4 perennial grasses, Andropogon gerardii and Sorghastrum nutans, frequently codominate areas of the mesic tallgrass prairie of the US Great Plains. A subtle difference in their vegetative reproduction strategies may play a role in preventing exclusion of S. nutans, the presumed weaker competitor in this region. 2. While A. gerardii vegetative tiller densities peak in the early growing season and decline thereafter (determinate recruitment), those of S. nutans may continue to increase throughout the growing season (indeterminate recruitment), providing a potential avenue for recovery from more intensive early season competition. However, until now these patterns have only been informally observed in the field. 3. We examined the year-to-year consistency of growing season vegetative tiller dynamics (measured as seasonal change in tiller densities) of each grass species from at an intact tallgrass prairie in Kansas - a site within the core of both species' distributions - over a period of 8 years. Then, to investigate environmental effects on these dynamics, we examined whether they differ across a Kansas landscape varying in topography, fire management regimes and the abundances of the study species. Finally, we expanded the investigation of environmental effects on growing season tiller dynamics by observing them at the periphery of the species' distributions in central Colorado, where climatic conditions are dryer and the study species' abundances are reduced. 4. Synthesis: We found that the tiller densities of A. gerardii decline within seasons with striking consistency regardless of spatio-temporal scale or environmental factors (topography and fire regimes). In contrast, we found the seasonal dynamics of S. nutans tiller densities were dependent on environmental factors, with seasonal tiller density increases occurring only within the Kansas populations but not consistently between years. These observations lay the groundwork for establishing differences in tiller recruitment determinacy as a potentially important yet underappreciated mechanism for promoting coexistence and codominance among perennial plant species.