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Revealing nanoscale plasticity of metallic nanosponges with correlative and scale-bridging 3D microscopy and modelling
<p>Data for manuscript "Revealing nanoscale plasticity of metallic nanosponges with correlative and scale-bridging 3D microscopy and modelling":</p> <p>SI Movies 01-12. Movies from Supporting Information. Description in file name.</p>
Online repository for Paper "AgentFL: Scaling LLM-based Fault Localization to Project-Level Context"
<h3>Summary</h3> <p>This is the online repository for the arXiv paper "AgentFL: Scaling LLM-based Fault Localization to Project-Level Context".</p> <p>We also provide the results for the TSE'25 paper "SOAPFL: A Standard Operating Procedure for LLM-based Method-Level Fault Localization".</p> <h3>Environment</h3> <ul> <li><a href="https://github.com/rjust/defects4j/tree/v1.4.0">Defects4J-V1.4.0</a> (Note that the buggy items in V1.4.0 is identical with V1.2.0, we use V1.4.0 to avoid some problems in V1.2.0)</li> <li><a href="https://github.com/rjust/defects4j/tree/v2.0.0">Defects4J-V2.0.0</a></li> <li>Python version >= 3.8.5</li> </ul> <h3>Defects4J Mod</h3> <p>Before running AgentFL, please apply the files under the <code>AgentFL/Defects4J_mod</code> directory to modify your Defects4J V1.4.0/V2.0.0.</p> <h3>Run AgentFL</h3> <p>Set your own OpenAI API key in <code>AgentFL/camel/model_backend.py</code></p> <p>It's easy to run AgentFL for localizing a bug with the following command:</p> <p><code>python3 run.py --config <CONFIG_DIR> --version <D4J_VERSION> --project <PROJECT> --bugID <BUG_ID> --model <GPT_MODEL_NAME></code></p> <p>For example:</p> <p><code>python3 run.py --config Default --version 1.4.0 --project Closure --bugID 26 --model GPT_3_5_TURBO</code></p> <p>More configs can be seen under the directory <code>AgentFL/Config</code></p> <h3>Results</h3> <p>We release all of the results of AgentFL in the <code>AgentFL/Results</code> directory, including the evaluation results on Defects4J V1.4.0/V2.0.0 and the ablation study result.</p> <p>For each bug, we record all of the prompts, responses, and intermediate outputs.</p> <blockquote> <p>NEW: We have released the newest results for TSE'25 paper "SOAPFL: A Standard Operating Procedure for LLM-based Method-Level Fault Localization". The results can be found in the `<a href="https://zenodo.org/api/records/16938304/draft/files/SoapFL_results.zip/content" target="_blank" rel="noopener noreferrer">SoapFL_results.zip</a>` file!</p> </blockquote> <h3>Human Evaluation Results</h3> <p>The human evaluation results can be found in the file <code>AgentFL/EvaluationResult/DebugResult_d4j140_GPT35_human.xlsx</code></p> <h3>System Messages for Agents</h3> <ul> <li>Test Code Reviewer:</li> </ul> <blockquote> <p>You are a Test Code Reviewer. We share a common interest in collaborating to successfully locate the buggy code that cause the test suite to fail. You can examine the test code and the initialized classes to analyze the similar behavior of the failed tests within the test suite. To locate the bug, you must write a response that appropriately solves the requested instruction based on your expertise.</p> </blockquote> <ul> <li>Source Code Reviewer</li> </ul> <blockquote> <p>You are a Source Code Reviewer. we are both working at DebugDev. We share a common interest in collaborating to successfully locate the buggy code that cause the test suite to fail. Your main responsibilities is to generate a comment for each covered method base on the method call relationship. To locate the bug, you must write a response that appropriately solves the requested instruction based on your expertise.</p> </blockquote> <ul> <li>Software Test Engineer</li> </ul> <blockquote> <p>You are a Software Test Engineer. We share a common interest in collaborating to successfully locate the buggy code that cause the test suite to fail. You main responsibilities include examining the information of the failed tests to analyze the possible causes of the test failures, and determining the method that need to be fixed. To locate the bug, you must write a response that appropriately solves the requested instruction based on your expertise.</p> </blockquote> <ul> <li>Software Architect</li> </ul> <blockquote> <p>You are a Software Architect. We share a common interest in collaborating to successfully locate the buggy code that cause the test suite to fail. You are very familiar with the architecture of the software, the functions of each class and method in the software. You main responsibilities include examining the given information to locate the possible buggy classes and buggy methods. To locate the bug, you must write a response that appropriately solves the requested instruction based on your expertise.</p> </blockquote>
Codes and data: Community size predicts temporal β-diversity at local but not regional scales
<p>UPDATED VERSION 2025-08-30 (models were updated)</p> <p>This zip file contains the codes demonstrating how I analyzed and selected publicly available and globally extensive data on fish composition and environmental variables to test the hypothesis that random fluctuations caused by demographic stochasticity in small populations might extend to communities and metacommunities, potentially affecting stability propagation across biological levels and spatial scales. The READ_ME file contains additional details about the steps I took to develop this analysis.</p> <p>This study was financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES) - Finance Code 001.</p>
microbetag : building a thorough database of genome-scale KO annotations
<p>In this repository we keep internal data for the <em><a href="https://hariszaf.github.io/microbetag/">microbetag</a> </em>microbial co-occurrence network annotator.</p> <p><em>microbetag</em> makes use of 2-column files for each genome, indicating the KO term found and a KEGG module in which this terms takes part into. <br>As a single KO term might participates in more than one KEGG modules, the same KO might be more than once in an annotation file. </p> <table> <tbody> <tr> <td> <div>chem_xref.tar.gz</div> </td> <td> <p>The MNXref namespace</p> <ol> <li>The identifier of a chemical compound in an external resource [<a href="https://www.metanetx.org/mnxdoc/mnxref.html#XREF">XREF</a>]</li> <li>The corresponding identifier in the MNXref namespace [<a href="https://www.metanetx.org/mnxdoc/mnxref.html#MNX_ID">MNX_ID</a>]</li> <li>The description given by the external resource [<a href="https://www.metanetx.org/mnxdoc/mnxref.html#STRING">STRING</a>]</li> </ol> <p>MNXref 4.0 release notes: - The third column (evidence tag for the mapping) was suppressed - The descriptions were completed - Deprecated identifiers were moved into they own table below</p> </td> </tr> <tr> <td> <div>gtdb_modelseed_gems.zip</div> </td> <td> <p>for all the GTDB genomes their corresponding <a href="https://patricbrc.org/">PATRIC</a> annotations were gathered. Then, using <a href="https://github.com/ModelSEED/ModelSEEDpy">modelseedpy</a> we constructed their genome scale metabolic reconstructions</p> </td> </tr> <tr> <td> <div>gtdb_kofam_scan_per_module.tar.gz</div> </td> <td> <p>all representative genomes of <a href="https://gtdb.ecogenomic.org/">GTDB</a> (v.202) were parsed and their corresponding `.faa` files were retrieved from the <a href="https://ftp.ncbi.nlm.nih.gov/genomes/all/">NCBI FTP</a>. Then the <a href="https://github.com/takaram/kofam_scan">kofam_scan</a> tool was used to annotate them and finally a <a href="https://github.com/hariszaf/microbetag/blob/clean/mappings/gtdb_mappings/gtdb_annotations_per_module.py">manual script </a>was used to keep KOs of each genome per module. </p> </td> </tr> <tr> <td>SeedSet.pkl.gz</td> <td> <p>A pickle file with the seeds of each GEM included in the <em>gtdb_modelseed_gems.zip </em>file and related to the KEGG MODULES based on the <em>seedId_keggId_module.tsv </em>file you can find on microbetag's GitHub page. Example:</p> <p>PATRIC SeedSet<br>373.172 [cpd00891, cpd00136, cpd00199, cpd01772, cpd00...<br>397278.5 [cpd00891, cpd00136, cpd01772, cpd02698, cpd08...</p> </td> </tr> <tr> <td>NonSeedSet.pkl.gz</td> <td> <p>A pickle file with the non seeds of each GEM included in the <em>gtdb_modelseed_gems.zip </em>file and related to the KEGG MODULES based on the <em>seedId_keggId_module.tsv </em>file you can find on microbetag's GitHub page. Example:</p> <p>PATRIC NonSeedSet<br>64187.548 [cpd00508, cpd00869, cpd00774, cpd03830, cpd00...<br>74426.1719 [cpd00204, cpd00447, cpd20171, cpd03470, cpd00...</p> </td> </tr> <tr> <td>seeds_per_genome.pkl.gz</td> <td> <p>A pickle file with a binary representation of the seeds per genome . Example:</p> <p> cpd00493 cpd00296 cpd11431 cpd00063 cpd15717 ... <br>2162051.4 1 0 0 1 0 0 0 0 0 0 ... </p> </td> </tr> <tr> <td> <div>nonseeds_per_genome.pkl.gz</div> </td> <td>Like above for non-seeds.</td> </tr> <tr> <td> <div>phen_classes.zip</div> </td> <td>A list of pickle files with the re-trained classes of phenDB for the prediction of functional traits on a genome.</td> </tr> </tbody> </table> <p> </p> <p> </p> <p> </p> <p> </p>
Output files for Degassing of CO2 triggers large-scale loss of helium from magma oceans
<p>This upload includes output files for the paper Degassing of CO2 triggers large-scale loss of helium from magma oceans.</p>
Data set for analyzing scaling and criticality in large-scale social systems regulated by global factors
<ul><li><strong>Research information</strong>:<ul><li>Title: Scaling and criticality in large-scale social systems regulated by global factors</li><li>Abstract: How do individuals in large-scale social systems behave in response to global factors and what kinds of macroscopic dynamics will emerge as consequences? Here we conduct a naturalistic observation of the daily consumer behaviours of 190,000 individuals from January 2018 to December 2022, extracting the long-term consumption dynamics of about 6000 types of commodities from approximately 2.2 million purchase orders. The consumption dynamics is subdivided into trend, seasonal, and random components, whose dynamic processes across scales are analyzed by a renormalization group. we discover that the coronavirus pandemic, an exogenetic factor acting on the social system, regulates the scaling and criticality of consumption dynamics. On a large time scale, the long-term dynamics of the system, regardless of arising from trend, seasonal, or random individual behaviours, is pushed towards a boundary between independent and correlated phases as the pandemic erupts. On a smaller time scale, short-term consumption dynamics exhibits more diversities in response to the pandemic. While the trend and random behaviours of individuals are driven to quasi-criticality and exhibit scale-invariance as the pandemic breaks out, seasonal behaviours are more robust against regulations. Overall, our study provides insights into the regulation mechanisms of global factors on the dynamics of large-scale and heterogeneous social systems.</li></ul></li><li><strong>Data set description</strong>:<ul><li>RawData: A csv file for approximately 2.2 million times purchase orders made by around 190,000 individuals before, during, and after the outbreak of coronavirus disease 2019 (COVID-19). </li><li>ConsumptionDynamics: A csv file that describes the daily evolution of the consumption frequencies for approximately 6,000 types of commodities. Each row denotes an extracted time series that measures the number of times a commodity is purchased each day. Each column denotes a single day.</li><li>Note that the names of commodities in current data set are writen in Chinese. </li></ul></li></ul><p> </p><p> </p>
King Rail (Rallus elegans) presence in the Midwestern United States is predicted by local-scale factors and avian community
Open the record for dataset details and reuse information.
Online appendix to State of the CArt: Evaluating Covering Array generators at scale
<p>This dataset includes the input models, figures, and resulting output of all CA generation tools evaluated in the context of the article "State of the CArt: Evaluating Covering Array generators at scale".</p><p>The file `models.tar.gz` includes the 295 input parameter models in four different dialects (ACTS, CTWedge/pMEDICI, PICT, and CASA).</p><p>The file `figures.zip` contains the underlying data of the figures included in the article and the resulting figures (as well as a number of additional visualizations that were not used in the published work).</p><p>The files beginning with `evaluation` contain the output, timing, and error messages produced by each of the competing tools, in one folder per strength (named after a timestamp in ascending order of strength).<br>In each of these folders, files conform to the following syntax:[toolname]_[model_filename]_[strength]_[iteration].[suffix]<br>where "toolname" is identical to the current folder,<br>"model_filename" is the exact name of the model file (including suffix),<br>"strength" is the combinatorial strength of the resulting CA (between 2 and 5),<br>"iteration" takes values between 1 and 3 and refers to the round of execution (at lower strengths, tools were tested using 3 iterations; at higher strengths, some tools required too much execution time and were only run once),<br>"suffix" is one of the following: "time" for the output of GNU time in verbose mode; "out" for the resulting CA (in headerless CSV form); "err" for the standard output (usually empty). Note that additional intermediate files may exist for some tools (e.g. when their original output is not strictly a headerless CSV).</p><p>All tools were executed in Docker containers based on the official OpenJDK image, which is itself based on Debian Buster (Docker identifier: openjdk:14-buster). The experiments were performed on a machine using a Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz (16 physical cores, 32 logical cores) with 256 GB RAM.</p><p>CASAConverterCLI.jar is a standalone Java program that converts CTWedge models to CASA models. It accepts the path to a CTWedge model and the strength as its parameters.</p><p>ct-eval-framework.tar.bz2 contains the evaluation framework itself. It can be used to replicate our results and evaluate your own CA generator. Setup instructions are provided in the README.md file wihtin the archive.</p><p>wca-gcc-11-fix.patch is a patch that enables the compilation of WCA under newer versions of GCC.</p>
FIGURE 105. Stephanomia amphytridis. A. Palpon and palpacle. Scale bar 5 in A review of the physonect siphonophore genera Halistemma (Family Agalmatidae) and Stephanomia (Family Stephanomiidae)
FIGURE 105. Stephanomia amphytridis. A. Palpon and palpacle. Scale bar 5 mm. B. Portion of palpacle showing attached nematocysts. Scale bar 100 µm. C. Nematocyst. Scale bar 10 µm.
FIGURE 57. Halistemma transliratum Nectalia-stage paratype specimen from JSLII Dive 972. Scale bar 5 in A review of the physonect siphonophore genera Halistemma (Family Agalmatidae) and Stephanomia (Family Stephanomiidae)
FIGURE 57. Halistemma transliratum Nectalia-stage paratype specimen from JSLII Dive 972. Scale bar 5 mm.
FIGURE 54. Halistemma transliratum. Type A bracts—upper views. Scale 5 in A review of the physonect siphonophore genera Halistemma (Family Agalmatidae) and Stephanomia (Family Stephanomiidae)
FIGURE 54. Halistemma transliratum. Type A bracts—upper views. Scale 5 mm. Redrawn from Pugh & Youngbluth (1988).
FIGURE 2. Anterior lateral-line scale 12 in Sunagocia omanensis, a new flathead fish (Scorpaeniformes, Platycephalidae) from the Western Indian Ocean, with comments on the distribution of Sunagocia carbuncula
FIGURE 2. Anterior lateral-line scale 12 (length 2.3 mm) from right side of holotype of S. omanensis, BPBM 36045.
FIGURE 9 in Scale surface microstructure and scale size in the tooth-carp genus Aphanius (Teleostei, Cyprinodontidae) from endorheic basins in Southwest Iran
FIGURE 9. Dendrogram based on the between-groups-linkage method showing the phenotypic relations among the studied populations of Aphanius sophiae (Kor River Basin), A. farsicus (Maharlu Lake Basin) and A. pluristriatus (Mond River Basin). The dendrogram is based on all characters of the scale surface morphology and microstructures (see Tables 2 and 3). I: Kor River subsystem and II: Tashk and Bakhtegan Lakes subsystem. See Table 1 for codes of sampling sites.
FIGURE 5 in Scale surface microstructure and scale size in the tooth-carp genus Aphanius (Teleostei, Cyprinodontidae) from endorheic basins in Southwest Iran
FIGURE 5. Scale surface microstructures of the studied species: First circuli on the rostral field. A–I: Aphanius sophiae from the Kor River subsystem (A—Safashahr, B—Ghadamgah, C—Beyza, D—Bandeamir, E—Kharameh) and from the Tashk and Bakhtegan Lakes subsystem (F—Gomban, G—Tashk, H—Bakhtegan, I—Gol); J–M: A. farsicus from the Maharlu Lake Basin (J—Dobaneh, K—Pirbanoo, L—Babunak, M—Barmeshoor); N: A. pluristriatus from Zarjan in the Mond River Basin. Arrows indicate continuous circuli. Scale bar: 20 µm.
FIGURE 6 in Scale surface microstructure and scale size in the tooth-carp genus Aphanius (Teleostei, Cyprinodontidae) from endorheic basins in Southwest Iran
FIGURE 6. Scale surface microstructures of the studied species: Tubercles on the caudal scale field. A–I: Aphanius sophiae from the Kor River subsystem (A—Safashahr, B—Ghadamgah, C—Beyza, D—Bandeamir, E—Kharameh) and from the Tashk and Bakhtegan Lakes subsystem (F—Gomban, G—Tashk, H—Bakhtegan, I—Gol); J–M: A. farsicus from the Maharlu Lake Basin (J—Dobaneh, K—Pirbanoo, L—Babunak, M—Barmeshoor); N: A. pluristriatus from Zarjan in the Mond River Basin. Arrows in E and L show mucus pores. Scale bar: 20 µm.
FIGURE 2. A in Scale surface microstructure and scale size in the tooth-carp genus Aphanius (Teleostei, Cyprinodontidae) from endorheic basins in Southwest Iran
FIGURE 2. A) Schematic drawing of an Aphanius scale, including some of the terms used in this study. Terminology follows Lippitsch (1990), Kuusipalo (1998), Jawad (2005) and Jawad and Al-Jufaili (2007). Dashed lines delimit the different fields. Scale bar: 200 µm. B) Measurements of scale length and width (after Esmaeili 2001). C) Schematic shapes of scale and focus as described in this study and in Table 3; terminology follows Kuusipalo (1998): a—Pentagonal, b—Elliptic-pentagonal, c—Round-pentagonal, d—Round-triangular, e—Elliptic-rectangular, f—Oblong, g—Oval, h—Round, i—Quadrangular, j—Rectangular, k—Trapezoidal, l—Elliptical.
FIGURE 1 in Scale surface microstructure and scale size in the tooth-carp genus Aphanius (Teleostei, Cyprinodontidae) from endorheic basins in Southwest Iran
FIGURE 1. Geographic overview and position of the study sites; numbers 1–5 refer to Aphanius sophiae from the Kor River subsystem (1—Safashahr, 2—Ghadamgah, 3—Beyza, 4—Bandeamir, 5—Kharameh), 6–9 refer to A. sophiae from the Tashk and Bakhtegan Lakes subsystem (6—Gomban, 7—Tashk, 8—Bakhtegan, 9—Gol), 10–13 refer to A. farsicus from the Maharlu Lake Basin (10—Dobaneh, 11—Pirbanoo, 12—Babunak, 13—Barmeshoor), and 14 is A. pluristriatus from Zarjan in the Mond River Basin.
FIGURE 8 in Scale surface microstructure and scale size in the tooth-carp genus Aphanius (Teleostei, Cyprinodontidae) from endorheic basins in Southwest Iran
FIGURE 8. Scale surface microstructures of the studied species: Lepidonts on the lateral scale fields. A–I: Aphanius sophiae from the Kor River subsystem (A—Safashahr, B—Ghadamgah, C—Beyza, D—Bandeamir, E—Kharameh) and from the Tashk and Bakhtegan Lakes subsystem (F—Gomban, G—Tashk, H—Bakhtegan, I—Gol); J–M: A. farsicus from the Maharlu Lake Basin (J—Dobaneh, K—Pirbanoo, L—Babunak, M—Barmeshoor); N: A. pluristriatus from Zarjan in the Mond River Basin. Scale bar: 2 µm.
FIGURE 4 in Scale surface microstructure and scale size in the tooth-carp genus Aphanius (Teleostei, Cyprinodontidae) from endorheic basins in Southwest Iran
FIGURE 4. Scale surface microstructures of the studied species: Focus shapes and types of granules. A–I: Aphanius sophiae from the Kor River subsystem (A—Safashahr, B—Ghadamgah, C—Beyza, D—Bandeamir, E—Kharameh) and from the Tashk and Bakhtegan Lakes subsystem (F—Gomban, G—Tashk, H—Bakhtegan, I—Gol); J–M: A. farsicus from the Maharlu Lake Basin (J—Dobaneh, K—Pirbanoo, L—Babunak, M—Barmeshoor); N: A. pluristriatus from Zarjan in the Mond River Basin. Scale bar: 20 µm.
FIGURE 7 in Scale surface microstructure and scale size in the tooth-carp genus Aphanius (Teleostei, Cyprinodontidae) from endorheic basins in Southwest Iran
FIGURE 7. Scale surface microstructures of the studied species: Lepidonts on the rostral scale field. A–I: Aphanius sophiae from the Kor River subsystem (A—Safashahr, B—Ghadamgah, C—Beyza, D—Bandeamir, E—Kharameh) and from the Tashk and Bakhtegan Lakes subsystem (F—Gomban, G—Tashk, H—Bakhtegan, I—Gol); J–M: A. farsicus from the Maharlu Lake Basin (J—Dobaneh, K—Pirbanoo, L—Babunak, M—Barmeshoor); N: A. pluristriatus from Zarjan in the Mond River Basin. Scale bar: 2 µm.
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