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Data, Pre- and Post- processing scripts for shallow-water photogrammetry applications
<h1>Description</h1> <p>This repository contains the data and scripts to reproduce the results of Casella et al. (Remote Sensing, 2024). The scripts are in python, two of them are wrapped in Jupyter Notebooks with explanatory notes.<br><br>Please read the paper for further information on the platform used to collect the data shared in this repository.</p> <h2>Folder structure</h2> <p>The main folder contains two subfolders:</p> <ol> <li><strong>Data</strong>: this folder includes all the original data, and the results of the preprocessing and post-processing notebooks. Note that the original photos, included in the "Camera/all_photos" folder must be unzipped before running the preprocessing Jupyter Notebooks.</li> <li><strong>Precision_Analysis</strong>: this folder includes the digital bathymetric models that were co-registered as described in the paper. The co-registration was done offline with Quantum GIS. In this folder are also stored the results of the "Compare_DBMs.py" script, that makes the precision analysis (differences between co-registered DBMs).</li> </ol> <h2>Installation</h2> <p>Refer to the README.md file for a quick installation guide using Anaconda. </p> <h2>Credits</h2> <p>The code included in this work has been improved with the assistance of ChatGPT, which provided guidance on optimization, debugging, and documentation to enhance clarity and functionality. All the code has been reviewed and supervised by humans to ensure consistency and correctness.</p>
Fig. 3 in Exogenous application of polyamines alleviates water stress-induced oxidative stress of Rosa damascena Miller var. trigintipetala Dieck
Fig. 3. Effects of foliar application of spermine (Spm) and spermidine (Spd) on A: CAT and B: SOD activities of Rosa damascena Miller var. trigintipetala Dieck leaves grown under water stress (50% FC) or non-stress (100% FC) conditions. Columns had different letters are significantly differ from each other according to Duncan multiple range test at P = 0.05 (n = 8).
Fig. 2 in Exogenous application of polyamines alleviates water stress-induced oxidative stress of Rosa damascena Miller var. trigintipetala Dieck
Fig. 2. Effects of foliar application of spermine (Spm) and spermidine (Spd) on A: proline content, B: H2O2 content, C: MAD content and D: MSI (%) of Rosa damascena Miller var. trigintipetala Dieck leaves grown under water stress (50% FC) or non-stress (100% FC) conditions. Columns had different letters are significantly differ from each other according to Duncan multiple range test at P = 0.05 (n = 8).
Fig. 1 in Exogenous application of polyamines alleviates water stress-induced oxidative stress of Rosa damascena Miller var. trigintipetala Dieck
Fig. 1. Effects of foliar application of spermine (Spm) and spermidine (Spd) on A: relative water content (RWC %), B: stomatal conductance and C: total chlorophyll content of Rosa damascena Miller var. trigintipetala Dieck plant grown under water stress (50% FC) or nonstress (100% FC) conditions.Columns had different letters are significantly differ from each other according to Duncan multiple range test at P = 0.05 (n = 8).
User Experience Analysis of Jak Lingko Application Using Honeycomb UX Method with Smart PLS
<p><strong><em>Abstract— </em></strong>As a growing capital city, Jakarta has seen an increase in the use of public transportation such as Trans Jakarta, MRT, LRT, and KRL. These intermodal modes of transportation have become the main choice for people of Jakarta in carrying out their daily activities. To support the integration of various modes of transportation, the government through the Ministry of Transportation developed a smart transportation ecosystem based on the Jak Lingko application. Although this application has great potential in reducing congestion, the low rating of the application indicates a need for further evaluation. This study aims to analyze the level of user satisfaction with the Jak Lingko application in terms of user experience and identify areas that require improvement. A quantitative approach with a survey method was used to measure the quality of the Jak Lingko application user experience. The questionnaire was designed based on Honeycomb's UX framework which includes seven aspects: useful, usable, findable, accessible, credible, desirable, and valuable. The results show that the measurement model has good reliability and validity, with Cronbach's alpha values ranging from 0.843 to 0.945 and average AVE values above 0.5. Path analysis shows that accessibility has a significant influence on the perceived added value of the app. These findings highlight the importance of accessibility in improving the user experience of public transportation applications.</p> <p><strong><em>Keywords - </em></strong>user experience, mobile application, public transportation, Honeycomb framework, Jak Lingko, Smart PLS.</p>
Data from: Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally-invasive DNA samples to support studies in molecular ecology
Minimally-invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping-by-sequencing approaches, which have been traditionally developed for high-quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping-in-Thousands by sequencing (GT-seq), a multiplex amplicon sequencing approach, to effectively genotype minimally-invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT-seq from a de novo restriction-site associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT-seq for the same individuals found low rates of genotyping error (GT-seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT-seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT-seq and RADseq datasets, as were inferred patterns of population structure. Overall, GT-seq can be effectively applied to low quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally-invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era.
Data from: Testing the role of climate in speciation: new methods and applications to squamate reptiles (lizards and snakes)
Climate may play important roles in speciation, such as causing the range fragmentation that underlies allopatric speciation (through niche conservatism) or driving divergence of parapatric populations along climatic gradients (through niche divergence). Here, we developed new methods to test the frequency of climate niche conservatism and divergence in speciation, and applied it to species pairs of squamate reptiles (lizards and snakes). We used a large-scale phylogeny to identify 242 sister-species pairs for analysis. From these, we selected all terrestrial allopatric pairs with sufficient occurrence records (n=49 pairs) and inferred whether each originated via climatic niche conservatism or climatic niche divergence. Among the 242 pairs, allopatric pairs were most common (41.3%), rather than parapatric (19.4%), partially sympatric (17.7%), or fully sympatric species pairs (21.5%). Among the 49 selected allopatric pairs, most appeared to have originated via climatic niche divergence (61–76%, depending on the details of the methods). Surprisingly, we found greater climatic niche divergence between allopatric sister species than between parapatric pairs, even after correcting for geographic distance. We also found that niche divergence did not increase with time, further implicating niche divergence in driving lineage splitting. Overall, our results suggest that climatic niche divergence may often play an important role in allopatric speciation, and the methodology developed here can be used to address the generality of these findings in other organisms.
Data from: A hybrid phylogenetic–phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification
Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using *BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for > 10 Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas.
Data from: Creating a multi-track classical music performance dataset for multi-modal music analysis: challenges, insights, and applications
We introduce a dataset for facilitating audio-visual analysis of musical performances. The dataset comprises 44 simple multi-instrument classical music pieces assembled from coordinated but separately recorded performances of individual tracks. For each piece, we provide the musical score in MIDI format, the audio recordings of the individual tracks, the audio and video recording of the assembled mixture, and ground- truth annotation files including frame-level and note-level tran- scriptions. We describe our methodology for the creation of the dataset, particularly highlighting our approaches for addressing the challenges involved in maintaining synchronization and ex- pressiveness. We demonstrate the high quality of synchronization achieved with our proposed approach by comparing the dataset against existing widely-used music audio datasets. We anticipate that the dataset will be useful for the devel- opment and evaluation of existing music information retrieval (MIR) tasks, as well as for novel multi-modal tasks. We bench- mark two existing MIR tasks (multi-pitch analysis and score- informed source separation) on the dataset and compare against other existing music audio datasets. Additionally, we consider two novel multi-modal MIR tasks (visually informed multi-pitch analysis and polyphonic vibrato analysis) enabled by the dataset and provide evaluation measures and baseline systems for future comparisons (from our recent work). Finally, we propose several emerging research directions that the dataset enables.
Database of the work "Sensitivity analysis as support for reliable life cycle cost evaluation an application on eleven nearly zero-energy buildings in Europe"
<p>This database reports the detailed results of the work "Sensitivity analysis as support for reliable life cycle cost evaluation an application on eleven nearly zero-energy buildings in Europe" published on the journal Sustainable Cities and Society.</p> <p>In particular, it includes the main sensitivity indices and life cycle cost values of eleven nZEB buildings across Europe as calculated within the H2020 project CRAVEzero (Cost Reduction and market Acceleration for Viable nearly zero-Energy buildings).</p> <p> </p>
FIGURE 2 in Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)
FIGURE 2. Box plots of selected characters showing mean (point), mean ± SD (box), and range of variation (bars) for Deyeuxia abnormis (abno), D. diffusa (diff), D. flaccida (flac), A. gigantea (gig), A. pleiophylla (plei) and A. zenkeri (zenk).
FIGURE 7 in Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)
FIGURE 7. The first syntype of Agrostis pleiophylla, Clarke 44736B (B). The left-hand specimen (covered by the label attached to the upper left-hand corner of the sheet) and the right-hand specimen are identified as Deyeuxia diffusa. The middle specimen is recognized as Agrostis pleiophylla.
FIGURE 6 in Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)
FIGURE 6. Inflorescence of Deyeuxia diffusa (CHINA: NW Yunnan, ca. 12 km E of Zhongdian (Shangrila), photograph: Beata Paszko).
FIGURE 4. Glumes and floret. A–B in Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)
FIGURE 4. Glumes and floret. A–B. Deyeuxia abnormis, Ohba et al. 62069 (TI); C–D. Deyeuxia diffusa, Kanai et al. 6302070 (TI). Scale bar = 1 mm.
FIGURE 3 in Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)
FIGURE 3. Lectotype of Deyeuxia abnormis designated by Bor (1954a) (K). Reproduced with permission from the Board of the Trustees of the RBG, Kew.
FIGURE 1 in Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)
FIGURE 1. Scatter plot of two ratios: callus hairs to lemma length against palea to lemma length, for Deyeuxia abnormis (open circles), D. diffusa (solid squares), D. flaccida (asterisks), Agrostis gigantea (open triangles), A. pleiophylla (solid triangles) and A. zenkeri (solid circle). Abbreviations: 1, Aulacolepis petelotii—holotype; 2, Anisachne gracilis—epitype selected in the present study; 3, Deyeuxia abnormis—lectotype selected by Bor (1954a); 4, Agrostis continentalis—lectotype selected in the present study; 5, A. zenkeri—holotype; 6, A. pleiophylla—lectotype selected by Noltie (1999); 7, Deyeuxia abnormis—lectotype selected by Noltie (1999); 8, D. diffusa—holotype; 9, D. flaccida—holotype; 10, Agrostis nagensis—holotype; 11, A. pleiophylla—lectotype selected in the present study.
Velocity, density and energy budget statistics from the article: Validation and application of the lattice Boltzmann algorithm for a turbulent immiscible Rayleigh-Taylor system
<p>We develop a multicomponent lattice Boltzmann (LB) model for the 2D Rayleigh--Taylor turbulence with a Shan-Chen pseudopotential implemented on GPUs. Accuracy of the LB model is tested both for early and late stages of instability. For the developed turbulent motion we analyze the balance between different terms describing variations of the kinetic and potential energies. Then, we analyze the role of interface in the energy balance, and also the effects of the vorticity induced by the interface in the energy dissipation. Statistical properties are compared for miscible and immiscible flows.</p> <p>In this Dataset, we have included the files for the statistics of the energy budget for the miscible and immiscible Rayleigh-Taylor flows studied in the referred article.</p> <p>We also included the examples of the density and velocity fields showed in the Figures 1 and 2 of the article.</p>
Effects of Application of Recycled Chicken Manure and Spent Mushroom Substrate on Organic Matter, Acidity, and Hydraulic Properties of Sandy Soils
<p>This study aimed at examining the effects of long-term application of<br> chicken manure (CM) and spent mushroom substrate (SMS) on organic matter accumulation, acidity,<br> and hydraulic properties of soil. Two podzol soils with sandy texture in Podlasie Region (Poland)<br> were enriched with recycled CM (10 Mg ha1) and SMS (20 Mg ha1), respectively, every 1–2 years<br> for 20 years. The application of CM and SMS increased soil organic matter content at the depths<br> of 0–20, 20–40, and 40–60 cm, especially at 0–20 cm (by 102–201%). The initial soil pH increased in<br> the CM- and SMS-amended soil by 1.7–2.0 units and 1.0–1.2 units, respectively. Soil bulk density at<br> comparable depths increased and decreased following the addition of CM and SMS, respectively.<br> The addition of CM increased field water capacity (at –100 hPa) in the range from 45.8 to 117.8%<br> depending on the depth within the 0–60 cm layer. In the case of the SMS addition, the value of the<br> parameter was in the range of 42.4–48.5% at two depths within 0–40 cm. Depending on the depth, CM<br> reduced the content of transmission pores (>50 m) in the range from 46.3 to 82.3% and increased the<br> level of residual pores (<0.5 m) by 91.0–198.6%. SMS increased the content of residual pores at the<br> successive depths by 121.8, 251.0, and 30.3% and decreased or increased the content of transmission<br> and storage pores. Additionally, it significantly reduced the saturated hydraulic conductivity at<br> two depths within 0–40 cm. The fitted unsaturated hydraulic conductivity at two depths within the<br> 0–40 cm layer increased and decreased in the CM- and SMS-amended soils, respectively. The results<br> provide a novel insight into the application of recycled organic materials to sequester soil organic<br> matter and improve crop productivity by increasing soil water retention capacity and decreasing<br> acidity. This is of particular importance in the case of the studied low-productivity sandy acidic soils<br> that have to be used in agriculture due to limited global land resources and rising food demand.</p>
Symbolic Automatic Relations and Their Applications to SMT and CHC Solving
<p>This is a replication package for the paper "Symbolic Automatic Relations and Their Applications to SMT and CHC Solving," published in the proceedings of the 28th Static Analysis Symposium (SAS 2021).</p> <p>This package contains all the tools discussed in the paper, and all the benchmarks the evaluation was conducted on, along with README.md and benchmark scripts.</p>
Green spectrofluorimetric assay of dantrolene sodium via reduction method: application to content uniformity testing
<p>The green analysis has turned out to be of a great value in all areas, including pharmaceutical analysis. Thus, it is extremely important to consider the environmental influence of each step in developing any analysis technique. The present work illustrates a validated, simple and green spectrofluorimetric method for the analysis of dantrolene sodium. The developed process is characterized by being of high sensitivity as well as being relatively inexpensive. The suggested technique based on the formation of a highly fluorescent product of dantrolene sodium via its reduction by the aid of Zn/HCl system. The resulting fluorophore showed a powerful fluorescence at λ<sub>em</sub> 344 nm after excitation at λ<sub>ex</sub> 279 nm. Calibration graph revealed a great linear regression (r = 0.9998) within concentration ranging from 0.05 to 2.0 µg mL<sup>−1</sup>. The suggested method had a very low detection and quantification limit of 0.007 ng mL<sup>−1</sup> and 0.019 ng mL<sup>−1</sup>, respectively. The applied technique was effectively used in the determination of dantrolene sodium in its pharmaceutical preparations. The results were compared with those from using the official USP method and they were in a good agreement. Moreover, content uniformity testing of dantrolene sodium in capsules was performed adopting the investigated technique with satisfying results. The greenness of the suggested technique was confirmed by the three standard assessment tools. Therefore, the developed technique can be used in the routine quality control analysis of dantrolene sodium with minimum harmful impact on nature or individuals.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.