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FIGURE 1 in Earthworms in the conversion of natural grasslands to agropastoral systems-a preliminary study in Vale Verde, Rio Grande do Sul, Brazil
FIGURE 1. The sites in the sampling dates: a) natural grassland (NG1) in July 2018, b) agropastoral system with soybean (AP) in December 2018, c) agropastoral system with winter crops (AP) in July 2019, d) the second natural grassland (NG2) in July 2019.
Conversation in forums: How software forum posts discuss potential software requirements
<p>User feedback on software usage is utilised to formulate software requirements, and software product forums are platforms rich in software-related user feedback. However, previous studies have mainly focused on analysing forum user feedback as individual sentences, which can lead to missing insights and a lacking understanding of the overall context of forum posts. This work examines software forum user feedback in forum posts to investigate the differences between sentence and post-level content analysis. We manually evaluated software forum posts collected from two open-sourced software forums and discovered five new types of user feedback that can only be identified in post-level analysis. Additionally, we examined the association between sentence classifications found within software forums. Our results indicate that contextual information related to requirements frequently appears with explicit requirement statements in forum posts. This information can be used to reduce the manual effort required to chase up missing contextual information when working through an issue. We also provide insights into the order of events happening in software product forums at the post level. Our findings reveal the importance of looking at forum-based user feedback at a post level to identify new insights on user feedback for requirements engineering.</p> <p> </p> <p>The file contains the post-level classification dataset created from this study as well as our heatmap figures for RQ2.</p>
Data for Thermoelectric conversion of deep-sea hydrothermal chimneys
<p>This is the data set for the paper 'Thermoelectric conversion of deep-sea hydrothermal chimneys'</p>
R notebooks to reproduce all analyses from the manuscript "grandR: a comprehensive package for nucleotide conversion sequencing data analysis"
<p>This package contains all R notebooks to reproduce the analyses from our manuscript "grandR: a comprehensive package for nucleotide conversion sequencing data analysis".</p> <p>In the zip file you find</p> <ul> <li>several rds files in the data folder: They contain grandR objects of both simulated and real SLAM-seq data sets. You can delete them and create them again by either just "knitting" the notebooks (which will generate all data necessary for this notebook and save it into the data folder), or by executing the generateAllDataFiles.R script ("Rscript generateAllDataFiles.R"), which will generate all rds files that do not exist).</li> <li>several R notebooks (Rmd): "Knitting" them will generate all figures from the manuscript. Without the data files (rds), this will be slow!</li> <li>knit_all.bash: Execute to "knit" all notebooks</li> <li>clean.bash: Clear the output of "knitting" the notebooks</li> </ul> <p> </p>
A nationwide collapse of a priority grassland bird related to livestock conversion and intensification
<p><span>Grassland birds are among the most threatened and fastest declining terrestrial vertebrate species in Europe, principally due to agricultural intensification and transformation. The little bustard is a priority grassland bird under the European Directive (2009/147/CE) that led to the classification of a network of Special Protected Areas (SPAs) in Portugal. A third national survey carried out in 2022 reveals a worsening of an ongoing population collapse at a national scale. The population declined by 77% and 56% compared to the previous surveys in 2006 and 2016, respectively. We found that the little bustard has greatly disappeared outside SPAs, while the remaining breeding population concentrated within the protected area network is showing a steep decline rate of 9% a year. This decline is now twice as fast when compared to the period 2006-2016. Analysis of the variation of the breeding densities between 2006 and 2022 at 49 survey sites revealed that those that initially had higher bustard densities and shifted toward a higher proportion of cattle among the total stocking rate experienced steeper declines. Areas where the density of roads increased also experienced declines over the course of the study period. Agricultural areas converted to or dominated by beef production likely relate to low breeding success and mortality of nesting females in fodder crops. Still, major habitat conversion outside SPAs to permanent crops led to overall habitat destruction, which contributed to the species decline and range contraction. Other threats are likely acting synergistically such as fragmentation, climate change and anthropogenic mortality. The extinction of the little bustard in Portugal is expected in the short term if no conservation actions are put in place.</span></p>
Data Repository for Chip-Chat: Challenges and Opportunities in Conversational Hardware Design
<p><strong># Data Repository for Chip-Chat: Challenges and Opportunities in Conversational Hardware Design</strong></p><p>This repository accompanies the manuscript accepted at MLCAD 2023, titled "Chip-Chat: Challenges and Opportunities in Conversational Hardware Design".</p><p>It contains the following:</p><p>- `free-chat-gpt4-tt03` - this contains the data used for the paper, which examines free-form process when exploring the potential applications for LLMs in hardware design. The task here was to generate the Verilog for a full (albeit small) processor design. Here, the chats are presented (and annotated) in the `/chats` subdirectory, which also includes a python script for extracting metadata (presented in table IV in the manuscript). Note that this directory also includes `/assembler` which provides a basic assembler (also written in Python) to make it easier to write demo programs (examples included) for the processor.</p><p>- `scripted-benchmarks` - this contains additional data not used in the paper, which examines a more rigid process when exploring the potential applications for LLMs in hardware design. Here, each model chats are separated by subdirectory.</p><p>- `scripted-benchmarks-gpt4-tt03` - this contains just the benchmarks not used in the paper, made by the first run of GPT-4, which were used for tapeout in Tiny Tapeout 3.</p><p>The two tt03 directories contain the GitHub action scripts required to invoke OpenLane and produce synthesis files, as well as used to perform simulation tests.</p>
Survey About "Conversion Therapy" in Canada
<p>The goal of this survey is to better understand the nature and scope of sexual orientation or gender identity or expression change efforts (SOGIECE), or “conversion therapy” in Canada. We define SOGIECE as any practice that attempts to deny, discourage, or delay feelings of sexual attraction to members of the same gender (e.g., felt identity as lesbian, gay, bisexual, queer [LGBQ], etc.), LGBQ identities, non-conforming gender expressions, or gender identities that differ from sex at birth (e.g., transgender).</p>
Conversation in forums: How software forum posts discuss potential development insights
<p>User feedback on software usage is utilised by developers to improve their software, and software product forums are platforms rich in software-related user feedback. However, previous studies have mainly focused on analysing forum user feedback as individual sentences, which can lead to missing insights and a lacking understanding of the overall context of forum posts. This work examines software forum user feedback in forum posts to investigate the differences between sentence and post-level content analysis. We manually evaluated software forum posts collected from two open-sourced software forums and discovered five new types of user feedback that can only be identified in the post-level analysis. Additionally, we examined the association between sentence classifications found within software forums. Our results indicate that contextual information complimenting product improvement insights can be found in software forums. This information can be used to reduce the manual effort required to chase up missing contextual information when working through an issue. We also provide insights into the progression of posts in software product forums at the thread level. Our findings reveal the importance of looking at forum-based user feedback at a post level to identify new insights on user feedback for software improvements.</p> <p> </p> <p>The file contains the post-level classification dataset created from this study as well as our coding guideline used for the process.</p>
On the Helpfulness of Answering Developer Questions on Discord with Similar Conversations and Posts from the Past
<p>Replication Package for "On the Helpfulness of Answering Developer Questions on Discord with Similar Conversations and Posts from the Past".</p>
Sensitivity analysis: ongoing and historical conversion therapy practices (CTPs) in Canada
<p>Sensitivity analysis: ongoing and historical conversion therapy practices (CTPs) in Canada</p>
Linear-to-Circular Polarization Conversion with Full-Silica Meta-Optics to Reduce Nonlinear Effects in High-Energy Lasers - Nature Com - Dataset
<p>Data from the Nature Communication paper entitled "Linear-to-Circular Polarization Conversion with Full-Silica Meta-Optics to Reduce<br> Nonlinear Effects in High-Energy Lasers"</p> <p>.OPJU files can be opened with ORIGINLab</p> <p>. MAT files can be opened with MATLAB/SCILAB</p>
Simulation dataset for "HORNET - A Power Density Quantifying Out of Thermodynamic Equilibrium Energy Conversion"
<p>Simulation dataset for reproducing figures used in the manuscript</p>
Degenerate photons from a cryogenic spontaneous parametric down-conversion source
<p>Dataset of the publication "Degenerate photons from a cryogenic spontaneous parametric down-conversion source", N. A. Lange, T. Schapeler, J. P. Höpker, M. Protte, and T. J. Bartley, <a href="https://doi.org/10.48550/arXiv.2303.17428">https://doi.org/10.48550/arXiv.2303.17428</a> (2023).</p> <p> </p> <p>Abstract:</p> <blockquote> <p>We demonstrate the generation of degenerate photon pairs from spontaneous parametric down-conversion in titanium-indiffused waveguides in lithium niobate at cryogenic temperatures. Since the phase matching cannot be temperature tuned inside a cryostat, we rely on a precise empirical model of the refractive indices when fabricating a fixed poling period. We design the phase-matching properties of our periodic poling to enable signal and idler photons at 1559.3(6) nm and characterize the indistinguishability of our photons by performing a Hong-Ou-Mandel interference measurement. Despite the effects of photorefraction and pyroelectricity, which can locally alter the phase matching, we achieve cryogenic indistinguishable photons within 1.5 nm of our design wavelength. Our results verify sufficient understanding and control of the cryogenic nonlinear process, which has wider implications when combining quasi-phase-matched nonlinear optical processes with other cryogenic photonic quantum technologies, such as superconducting detectors.</p> </blockquote>
Fig. 7 in Chemical identification of 18-hydroxycarlactonoic acid as an LjMAX1 product and in planta conversion of its methyl ester to canonical and noncanonical strigolactones in Lotus japonicus
Fig. 7. Conversion of [13C]-18-OH-MeCLA to [13C]-5DS and [13C]-lotuslactone (LL) in the feeding experiment using L. japonicus roots. A) Conversion of [10–13C]-18-OH-MeCLA to [6′-13C]-5DS. LC-MS/MS analysis of [6′-13C]-5DS in root exudates after feeding [10–13C]-18-OHMeCLA. MRM chromatograms (left) and full-scan spectra of fragment ions (right). The MRM chromatograms of authentic 5DS (red: 331.15/217.00, blue: 331.15/97.00, green: 331.15/234.00, m/z in positive mode) and [6′-13C]-5DS (red: 332.15/218.00, blue: 332.15/97.00, green: 332.15/ 235.00, m/z in positive mode) are shown. B) Conversion of [10–13C]-18- HO-MeCLA to [6′-13C]-LL. LC-MS/MS analysis of [6′-13C]-LL in root exudates after feeding [10–13C]-18-OH-MeCLA. MRM chromatograms (left) and full-scan spectra of fragment ions (right). The MRM chromatograms of authentic LL (red: 373.00/276.00, blue: 373.00/244.00, green: 373.00/ 216.00, m/z in positive mode) and [6′-13C]-LL (red: 374.00/277.00, blue: 374.00/245.00, green: 374.00/216.00, m/z in positive mode) are shown. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 8 in Chemical identification of 18-hydroxycarlactonoic acid as an LjMAX1 product and in planta conversion of its methyl ester to canonical and noncanonical strigolactones in Lotus japonicus
Fig. 8. The proposed biosynthetic pathway of 5DS and LL in L. japonicus. LjMAX1 catalyzes the oxidation of CL to 18-OH-CLA via CLA. (11R)-CL, CLA and 18- hydroxylated carlactonoates are precursors for 5DS and LL in L. japonicus. Solid arrows indicate confirmed pathways reported in previous studies and this study and dashed arrows indicate putative pathways. Blue letters indicate the position number. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6 in Chemical identification of 18-hydroxycarlactonoic acid as an LjMAX1 product and in planta conversion of its methyl ester to canonical and noncanonical strigolactones in Lotus japonicus
Fig. 6. Conversion of [13C]-CLA to [13C]-5DS and [13C]-18-OH-CLA in the feeding experiment using L. japonicus roots. A) Conversion of [1-13CH]- 3 CLA to [8-13CH]-5DS. LC-MS/MS analysis of [8-13CH]-5DS in root exu3 3 dates after feeding [1-13CH]-CLA. MRM chromatograms (left) and full3 scan spectra of fragment ions (right). The MRM chromatograms of authentic 5DS (red: 331.15/217.00, blue: 331.15/97.00, green: 331.15/ 234.00, m/z in positive mode) and [8-13CH]-5DS (red: 332.15/218.00, 3 blue: 332.15/97.00, green: 332.15/235.00, m/z in positive mode) are shown. B) Conversion of [1-13CH]-CLA to [1-13CH]-18-OH-CLA. LC-MS/ 3 3 MS analysis of [1-13CH]-18-OH-CLA in root exudates after feeding 3 [1-13CH]-CLA. MRM chromatograms (left) and full-scan spectra of frag3 ment ions (right). Authentic 18-OH-CLA was prepared by feeding CL to recombinant Os900. MRM chromatograms of authentic 18-OH-CLA (red: 347.00/303.00, blue: 347.00/113.00, m/z in negative mode) and [1-13CH]-18-OH-CLA (red: 348.00/304.00, blue: 348.00/113.00, m/z in 3 negative mode) are shown. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Chemical identification of 18-hydroxycarlactonoic acid as an LjMAX1 product and in planta conversion of its methyl ester to canonical and noncanonical strigolactones in Lotus japonicus
Fig. 3. Synthetic scheme of 13C-labeled and unlabeled 18-OH-MeCLA. Asterisks indicate the position of 13C.
Fig. 2 in Chemical identification of 18-hydroxycarlactonoic acid as an LjMAX1 product and in planta conversion of its methyl ester to canonical and noncanonical strigolactones in Lotus japonicus
Fig. 2. Detection of 18-hydroxycarlactonoic acid (18-OH-CLA), 4DO and 5DS in CLA feeding experiment by recombinant LjMAX1 and Os900. CLA was incubated with recombinant yeast microsomes. Yeast microsomes having an empty vector and the expression vector pYeDP60-Os900 were used as a negative and a positive control, respectively. The extracts of the microsomes and authentic standard were analyzed by LC-MS/MS. The peak at 7.0 min was presumed to be 18-OH-CLA which may be converted artificially to 4DO and 5DS in the ion source of mass spectrometer, and detected in the MRM transitions for 4DO and 5DS (red: 331.15/216.00, blue: 331.15/97.00, green: 331.15/234.00, m/z in positive mode). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Chemical identification of 18-hydroxycarlactonoic acid as an LjMAX1 product and in planta conversion of its methyl ester to canonical and noncanonical strigolactones in Lotus japonicus
Fig. 1. Detection of carlactonoic acid (CLA), 4-deoxyorobanchol (4DO) and 5- deoxystrigol (5DS) in carlactone (CL) feeding experiment by recombinant Lotus japonicus MAX1 (LjMAX1) and Os900. CL was incubated with yeast microsomes. Yeast microsomes having an empty vector and the expression vector pYeDP60-Os900 were used as a negative and a positive control, respectively. The extracts of the microsomes and authentic standard were analyzed by LCMS/MS. MRM chromatograms of CLA (red: 331.10/69.00, blue: 331.10/ 113.00, m/z in negative mode), 4DO and 5DS (red: 331.15/216.00, blue: 331.15/97.00, green: 331.15/234.00, m/z in positive mode) are shown. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Datasets for ``Magnetohydrodynamics predicts heavy-tailed distributions of axion-photon conversion''
<p>This directory contains an index.html file with links to the run<br> directories and idl plotting routines with secondary data for the other<br> figures for the paper "Magnetohydrodynamics predicts heavy-tailed<br> distributions of axion-photon conversion" by P. Carenza, R. Sharma,<br> M. C. D. Marsh, A. Brandenburg, & E. Mueller. If anything turns out to<br> be incomplete, please email brandenb@nordita.org.</p> <p>We provide details of the simulations of small-scale dynamo used for<br> the paper and provide also 3D snapshots of the magnetic fields for the<br> kinetic stage (bb8.dat) and the saturated stage (bb10.dat).</p> <p>Here, we also provide data files containing the probability of conversion<br> of photon to axion for MHD realization of the magnetic field. These<br> probabilities have been calculated using Eqs. (4) and (6) of our paper<br> and the data files bb8.dat and bb10.dat provided in the previous upload.<br> In data files relevant for Figs. 2, 5, and 6, the first and second<br> columns are the x and y coordinates, the third and fourth column<br> gives the probability of conversion for the linearly polarised light<br> in the y and x direction, respectively, and the fifth column gives the<br> probability for the unpolarised light. Additionally, we have data files,<br> "power_mag_bb8.dat" and "power_mag_bb10.dat," which contain data for<br> the magnetic field power spectra for the kinetic and saturated cases.</p> <p>Content:<br> ALP_MHD.zip (115.4 MB)<br> zip file with all run directories.</p> <p>bb10.dat (1.6 GB)<br> Run S, magnetic field as a single array, bb(512,512,512,3),</p> <p>bb10gau.dat (1.6 GB)<br> Gaussian magnetic field for Run S (same spectrum as bb10.dat)</p> <p>bb8.dat (1.6 GB)<br> Run K, magnetic field as a single array, bb(512,512,512,3),</p> <p>bb8gau.dat (1.6 GB)<br> Gaussian magnetic field for Run K (same spectrum as bb8.dat)</p> <p>D512_Pm20a2_bb8_versus_z.mpg (4.2 MB)<br> Anination of different z cross-sections for Run K</p> <p>D512_Pm20a2_versus_t.mpg (50.3 MB)<br> Anination of time evolution for Run S</p> <p>D512_Pm20a2_versus_z.mpg (5.8 MB)<br> Anination of different z cross-sections for Run S</p> <p>D512_Pm20a_gaussian9_versus_z.mpg (14.3 MB)<br> Anination of different z cross-sections for Gaussian version of Run K</p> <p>D512_Pm20a_gaussian_bb10_versus_z.mpg (9.5 MB)<br> Anination of different z cross-sections for Gaussian version of Run S</p> <p>D512_Pm20a_versus_t.mpg (19.3 MB)<br> Anination of time evolution for Run K</p> <p>rr10.dat (1.1 GB)<br> Density for Run S, rr(512,512,512).</p> <p>rr8.dat (1.1 GB)<br> Density for Run K, rr(512,512,512).</p> <p><br> Analysis files for figures (34.5 MB each)</p> <p>fig2a_bb8.dat<br> fig2b_bb8.dat<br> fig2c_bb8.dat</p> <p>fig2d_bb10.dat<br> fig2e_bb10.dat<br> fig2f_bb10.dat</p> <p>fig5a_bb8.dat<br> fig5b_bb10.dat</p> <p>fig6a_mask.dat<br> fig6b_clip.dat</p> <p>power_mag_bb8.dat (6 kB)<br> power_mag_bb10.dat (6 kB)</p>
ScienceDex guides
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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.