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zenodo32/100

Fig. 7 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 7. Relative expression analysis of LoTPS2 and LoTPS4 during different flower development performed by quantitative real-time PCR. (a, b) Transcript levels of the LoTPS2 and LoTPS4 genes during flower development. (c, d) Relative expression analysis of LoTPS2 and LoTPS4 at different flower developmental stages. Flower development was divided into 5 different stages: D1 (bud stage), D2 (little open), D3 (half open), D4 (full-bloom), D5 (senescence). GAPDH was used as an internal control. The root was set as 1. Data are presented as the mean ± SEM (n = 3).

opennotspecifiedMay 2020View details →
zenodo32/100

Fig. 8 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 8. Relative expression analysis of LoTPS genes and the emission of (E, E)-α-farnesene and D-limonene from Lilium 'Siberia' at different time intervals. (a, b) Expression pattern of LoTPS2 and LoTPS4 for 3 days postanthesis. (c) Emission pattern of (E, E)-α-farnesene from Lilium 'Siberia' (d) Emission pattern of D-limonene from Lilium 'Siberia' flowers over 3 days after full-bloom. The plants were kept under a 12 h light, 12 h dark photoperiod. GAPDH was used as an internal control. Each point is the average of 3 replicates.

opennotspecifiedMay 2020View details →
zenodo32/100

Fig. 6 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 6. (a) A labeled diagram of a fullbloom Lilium 'Siberia' flower. (b) Pictorial view of Lilium 'Siberia' flowers at different flower developmental stages.

opennotspecifiedMay 2020View details →
zenodo32/100

Fig. 5 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 5. Relative gene expression analysis of LoTPS2 and LoTPS4 in floraland vegetative tissues of Lilium 'Siberia' (a) relative expression levels of LoTPS2 in different tissues of Lilium 'Siberia' (b) Relative expression levels of LoTPS4 in different tissues of Lilium 'Siberia' analyzed by qRT-PCR. (c, d) Relative expression levels of LoTPS2 and LoTPS4 in full-bloom flowers of different Lilium species. GAPDH was used as an internal control. The highest expression level was set as 1 (100%). Lon: Longiflorum; Bru: Brunello; Sib: Siberia; Aca: Acapulco; Sor: Sorbonne; Man: Manissa. Data are presented as the mean ± SEM (n = 4).

opennotspecifiedMay 2020View details →
zenodo32/100

Fig. 1 in Molecular cloning, characterization and expression analysis of LoTPS2 and LoTPS4 involved in floral scent formation in oriental hybrid Lilium variety 'Siberia'

Fig. 1. (a) Alignment of the amino acid sequences of LoTPS2 and LoTPS4, with AdAFS1 from Actinidia deliciosa (FJ265785) and (+)-limonene synthase (Q8L5K3) from Citrus limon. The protein sequences were aligned using ClustalX 2.1 and edited with GeneDoc. RRX8W motifs were present in LoTPS4 and (+)-limonene synthase but were missing in both LoTPS2 and AdAFS1. The conserved RRX8W, DDXXD, and RxR domains are underlined. (b) N-terminal sequence alignment of TPS-f clade terpene synthases. AdAFS1; CbLIS2 (C. breweri, AAD19840); CbLIS (C. breweri, AAC49395); CcLIS (Clarkia concinna, AAD19839). The CDIS (conifer diterpene internal sequence) is indicated by a dotted line. Dashes indicate gaps inserted for optimal alignment. (c) Phylogenetic analysis of LoTPS2 and LoTPS4 from Lilium 'Siberia' with amino acid sequences of other selected terpene synthases. The alignment was performed using ClustalX 2.1, and the tree was built via the neighborjoining method using the MEGA 6 program and iTOL (http://itol.embl.de/). The dot size at the branches of the tree shows bootstrap values. Accession numbers are given in a Supplementary Table 1.

opennotspecifiedMay 2020View details →
zenodo32/100

Fig. 6. A in Molecular cloning and functional characterization of a two highly stereoselective borneol dehydrogenases from Salvia officinalis L

Fig. 6. A) Chemical reduction of racemic camphor leads to a mixture of four stereoisomers, from which SoBDH2 oxidizes three; B) Chemical reduction of (+)-camphor produces a mixture of (+)-1 (20%) and (−)-2 (80%), from which SoBDH1 oxidizes (+)-1 and leaves (−)-2 unreacted.

opennotspecifiedApr 2020View details →
zenodo32/100

Fig. 4. A in Molecular cloning and functional characterization of a two highly stereoselective borneol dehydrogenases from Salvia officinalis L

Fig. 4. A) Selective oxidative kinetic resolution of borneol enantiomers (+)-1 and (−)-1 and B) isoborneol enantiomers (+)-2 and (−)-2 to corresponding camphor enantiomers 3. The selective oxidation of (+)-borneol ((+)-1) leads to (+)-camphor ((+)-3), while selective oxidation of (+)-isoborneol leads to (−)-camphor (−)-3).

opennotspecifiedApr 2020View details →
zenodo32/100

Fig. 2 in Molecular cloning and functional characterization of a two highly stereoselective borneol dehydrogenases from Salvia officinalis L

Fig. 2. Phylogenetic analysis of SoBDH1, SoBDH2 and related ADHs. The tree was constructed using the neighbour-joining algorithm with Clustal O and visualized with Mega 7. Enzyme abbreviation, NCBI-accession number and species are following (enzymes used in this study marked in bold): LiBDH (LiBDH_0259) - borneol dehydrogenase from Levandula intermedia (AFV30207.1), AaBDH (AaBDH_0294) - borneol dehydrogenase from Artemisia annua (ANJ65952.1), ADH2 (AaADH_0265) - alcohol dehydrogenase from Artemisia annua (ADK56099.1), PsBDH (PsBDH_0261) - borneol dehydrogenase from Pseudomonas sp. TCU-HL1, SoBDH1 (SoBDH1_0259) - borneol dehydrogenase 1 from Salvia officinalis L., SoBDH2 (SoBDH2_0283) - borneol dehydrogenase 2 from Salvia officinalis L., PySDH_0270 - Secoisolariciresinol dehydrogenase from Prunus yedoensis var. nudiflora (PQQ15129.1), AaBDH2_0293 - borneol dehydrogenase from Artemisia annua (PWA65158.1), AaADH2_0265 - alcohol dehydrogenase from Artemisia annua (PWA54131.1), PpSCDH_0285 - putative short-chain dehydrogenase/reductase SDR from Pseudomonas putida (BAN13298.1). EgHYP_0318 - hypothetical protein MIMGU_mgv1a010226mg from Erythranthe guttata (EYU18089.1), DhSCDH_0290 - short chain alcohol dehydrogenase from Dorcoceras hygrometricum.

opennotspecifiedApr 2020View details →
zenodo32/100

Fig. 5 in Molecular cloning and functional characterization of a two highly stereoselective borneol dehydrogenases from Salvia officinalis L

Fig. 5. Kinetic characterization of the oxidation reaction of (+)-borneol catalyzed by SoBDH2. The lines represent the fit obtained using the Michaelis-Menten equation constructed using Origin 2017 software.

opennotspecifiedApr 2020View details →
zenodo32/100

Fig. 7 in Molecular cloning and functional characterization of a two highly stereoselective borneol dehydrogenases from Salvia officinalis L

Fig. 7. Enzymatic oxidation of different mixtures of enantiomers of 1 and 2. A) Oxidation of rac-1 after 24 h catalyzed by SoBDH1/SoBDH2; B) Oxidation of rac-2 after 24 h catalyzed by SoBDH1/SoBDH2. C) Oxidation of a mixture of rac-1 and rac-2 by SoBDH2. D) Oxidation reaction of a mixture of (+)-1 and (−)-2 (stemming from chemical reduction) of (+)-3) after 40 h.

opennotspecifiedApr 2020View details →
zenodo32/100

Fig. 3 in Molecular cloning and functional characterization of a two highly stereoselective borneol dehydrogenases from Salvia officinalis L

Fig. 3. Alignment of sequences of Salvia officinalis L. borneol dehydrogenases, SoBDH1 and SoBDH2 and other related plant ADHs. The sequences were aligned using Clustal O and visualized with Mega 7 (Sievers et al., 2014). NAD(H)-binding region is highlighted in a red square, catalytic residues (S, Y, K) highlighted in a blue square. Abbreviations of the enzymes is the same as in Fig. 2. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedApr 2020View details →
zenodo32/100

Fig. 1 in Molecular cloning and functional characterization of a two highly stereoselective borneol dehydrogenases from Salvia officinalis L

Fig. 1. Proposed pathway for (+)-camphor biosynthesis. BPC: (+)-bornyl pyrophosphate cyclase, BPPH: (+)-bornyl pyrophosphate hydrolase, BDH: (+)-borneol dehydrogenase.

opennotspecifiedApr 2020View details →
zenodo32/100

WIA-SZZ: Work Item Aware SZZ - Cloned Repository Files (6/7)

<p>For replication purposes, these 7 Zenodo&nbsp;records contain&nbsp;a copy&nbsp;of the cloned repositories from Rosa et. al, ICSE 2021, <a href="https://github.com/grosa1/icse2021-szz-replication-package">Evaluating SZZ implementations through a developer-informed oracle</a>, downloaded as of to Dec. 2022. These repositories were&nbsp;used for the&nbsp;evaluation and analysis of our paper&nbsp;WIA-SZZ: Work Item Aware SZZ. A script to download and unzip&nbsp;all&nbsp;files in these Zenodo records&nbsp;is provided as well.</p> <p>1. https://zenodo.org/record/8285106&nbsp; &nbsp; (doi: 10.5281/zenodo.8285106)<br> 2. https://zenodo.org/record/8285119&nbsp; &nbsp; (doi: 10.5281/zenodo.8285119)<br> 3. https://zenodo.org/record/8285121&nbsp; &nbsp; (doi: 10.5281/zenodo.8285121)<br> 4. https://zenodo.org/record/8285125&nbsp; &nbsp; (doi: 10.5281/zenodo.8285125)<br> 5. https://zenodo.org/record/8285127&nbsp; &nbsp; (doi: 10.5281/zenodo.8285127)<br> 6. https://zenodo.org/record/8285138&nbsp; &nbsp; (doi: 10.5281/zenodo.8285138)<br> 7. https://zenodo.org/record/8285140&nbsp; &nbsp; (doi: 10.5281/zenodo.8285140)</p>

openother-openAug 2023View details →
zenodo32/100

WIA-SZZ: Work Item Aware SZZ - Cloned Repository Files (7/7)

<p>For replication purposes, these 7 Zenodo&nbsp;records contain&nbsp;a copy&nbsp;of the cloned repositories from Rosa et. al, ICSE 2021, <a href="https://github.com/grosa1/icse2021-szz-replication-package">Evaluating SZZ implementations through a developer-informed oracle</a>, downloaded as of to Dec. 2022. These repositories were&nbsp;used for the&nbsp;evaluation and analysis of our paper&nbsp;WIA-SZZ: Work Item Aware SZZ. A script to download and unzip&nbsp;all&nbsp;files in these Zenodo records&nbsp;is provided as well.</p> <p>1. https://zenodo.org/record/8285106&nbsp; &nbsp; (doi: 10.5281/zenodo.8285106)<br> 2. https://zenodo.org/record/8285119&nbsp; &nbsp; (doi: 10.5281/zenodo.8285119)<br> 3. https://zenodo.org/record/8285121&nbsp; &nbsp; (doi: 10.5281/zenodo.8285121)<br> 4. https://zenodo.org/record/8285125&nbsp; &nbsp; (doi: 10.5281/zenodo.8285125)<br> 5. https://zenodo.org/record/8285127&nbsp; &nbsp; (doi: 10.5281/zenodo.8285127)<br> 6. https://zenodo.org/record/8285138&nbsp; &nbsp; (doi: 10.5281/zenodo.8285138)<br> 7. https://zenodo.org/record/8285140&nbsp; &nbsp; (doi: 10.5281/zenodo.8285140)</p>

openother-openAug 2023View details →
zenodo32/100

WIA-SZZ: Work Item Aware SZZ - Cloned Repository Files (1/7)

<p>For replication purposes, a copy of the cloned repositories from Rosa et. al, ICSE 2021, <a href="https://github.com/grosa1/icse2021-szz-replication-package">Evaluating SZZ implementations through a developer-informed oracle</a>&nbsp;(downloaded as of to Dec. 2022), used in our evaluation and analysis for our&nbsp;WIA-SZZ: Work Item Aware SZZ paper, is provided through 7 Zenodo links. A script to download and unzip them together is provided as well.</p> <p>1. https://zenodo.org/deposit/8285106&nbsp;&nbsp; &nbsp;doi: 10.5281/zenodo.8285106<br> 2. https://zenodo.org/deposit/8285119&nbsp;&nbsp; &nbsp;doi: 10.5281/zenodo.8285119<br> 3. https://zenodo.org/deposit/8285121&nbsp;&nbsp; &nbsp;doi: 10.5281/zenodo.8285121<br> 4. https://zenodo.org/deposit/8285125&nbsp;&nbsp; &nbsp;doi: 10.5281/zenodo.8285125<br> 5. https://zenodo.org/deposit/8285127&nbsp;&nbsp; &nbsp;doi: 10.5281/zenodo.8285127<br> 6. https://zenodo.org/deposit/8285138&nbsp;&nbsp; &nbsp;doi: 10.5281/zenodo.8285138<br> 7. https://zenodo.org/deposit/8285140&nbsp;&nbsp; &nbsp;doi: 10.5281/zenodo.8285140</p>

openother-openAug 2023View details →
zenodo32/100

WIA-SZZ: Work Item Aware SZZ - Cloned Repository Files (2/7)

<p>For replication purposes, these 7 Zenodo&nbsp;records contain&nbsp;a copy&nbsp;of the cloned repositories from Rosa et. al, ICSE 2021, <a href="https://github.com/grosa1/icse2021-szz-replication-package">Evaluating SZZ implementations through a developer-informed oracle</a>, downloaded as of to Dec. 2022. These repositories were&nbsp;used for the&nbsp;evaluation and analysis of our paper&nbsp;WIA-SZZ: Work Item Aware SZZ. A script to download and unzip&nbsp;all&nbsp;files in these Zenodo records&nbsp;is provided as well.</p> <p>1. https://zenodo.org/record/8285106&nbsp; &nbsp; (doi: 10.5281/zenodo.8285106)<br> 2. https://zenodo.org/record/8285119&nbsp; &nbsp; (doi: 10.5281/zenodo.8285119)<br> 3. https://zenodo.org/record/8285121&nbsp; &nbsp; (doi: 10.5281/zenodo.8285121)<br> 4. https://zenodo.org/record/8285125&nbsp; &nbsp; (doi: 10.5281/zenodo.8285125)<br> 5. https://zenodo.org/record/8285127&nbsp; &nbsp; (doi: 10.5281/zenodo.8285127)<br> 6. https://zenodo.org/record/8285138&nbsp; &nbsp; (doi: 10.5281/zenodo.8285138)<br> 7. https://zenodo.org/record/8285140&nbsp; &nbsp; (doi: 10.5281/zenodo.8285140)</p>

openother-openAug 2023View details →
zenodo32/100

WIA-SZZ: Work Item Aware SZZ - Cloned Repository Files (4/7)

<p>For replication purposes, these 7 Zenodo&nbsp;records contain&nbsp;a copy&nbsp;of the cloned repositories from Rosa et. al, ICSE 2021, <a href="https://github.com/grosa1/icse2021-szz-replication-package">Evaluating SZZ implementations through a developer-informed oracle</a>, downloaded as of to Dec. 2022. These repositories were&nbsp;used for the&nbsp;evaluation and analysis of our paper&nbsp;WIA-SZZ: Work Item Aware SZZ. A script to download and unzip&nbsp;all&nbsp;files in these Zenodo records&nbsp;is provided as well.</p> <p>1. https://zenodo.org/record/8285106&nbsp; &nbsp; (doi: 10.5281/zenodo.8285106)<br> 2. https://zenodo.org/record/8285119&nbsp; &nbsp; (doi: 10.5281/zenodo.8285119)<br> 3. https://zenodo.org/record/8285121&nbsp; &nbsp; (doi: 10.5281/zenodo.8285121)<br> 4. https://zenodo.org/record/8285125&nbsp; &nbsp; (doi: 10.5281/zenodo.8285125)<br> 5. https://zenodo.org/record/8285127&nbsp; &nbsp; (doi: 10.5281/zenodo.8285127)<br> 6. https://zenodo.org/record/8285138&nbsp; &nbsp; (doi: 10.5281/zenodo.8285138)<br> 7. https://zenodo.org/record/8285140&nbsp; &nbsp; (doi: 10.5281/zenodo.8285140)</p>

openother-openAug 2023View details →
zenodo32/100

WIA-SZZ: Work Item Aware SZZ - Cloned Repository Files (5/7)

<p>For replication purposes, these 7 Zenodo&nbsp;records contain&nbsp;a copy&nbsp;of the cloned repositories from Rosa et. al, ICSE 2021, <a href="https://github.com/grosa1/icse2021-szz-replication-package">Evaluating SZZ implementations through a developer-informed oracle</a>, downloaded as of to Dec. 2022. These repositories were&nbsp;used for the&nbsp;evaluation and analysis of our paper&nbsp;WIA-SZZ: Work Item Aware SZZ. A script to download and unzip&nbsp;all&nbsp;files in these Zenodo records&nbsp;is provided as well.</p> <p>1. https://zenodo.org/record/8285106&nbsp; &nbsp; (doi: 10.5281/zenodo.8285106)<br> 2. https://zenodo.org/record/8285119&nbsp; &nbsp; (doi: 10.5281/zenodo.8285119)<br> 3. https://zenodo.org/record/8285121&nbsp; &nbsp; (doi: 10.5281/zenodo.8285121)<br> 4. https://zenodo.org/record/8285125&nbsp; &nbsp; (doi: 10.5281/zenodo.8285125)<br> 5. https://zenodo.org/record/8285127&nbsp; &nbsp; (doi: 10.5281/zenodo.8285127)<br> 6. https://zenodo.org/record/8285138&nbsp; &nbsp; (doi: 10.5281/zenodo.8285138)<br> 7. https://zenodo.org/record/8285140&nbsp; &nbsp; (doi: 10.5281/zenodo.8285140)</p>

openother-openAug 2023View details →
zenodo32/100

Towards Human-interpretable Explanation in Code Clone Detection using LLM-based Post Hoc Explainer

<h2><strong>Overview</strong></h2> <div>This artifact accompanies the APSEC 2025 Research Track submission on <em>Towards Human-interpretable Explanation in Code Clone Detection using LLM-based Post Hoc Explainer</em>. The research focuses on using Large Language Models (LLMs) with local neighborhood sampling with in-context learning to provide explanations for GraphCodeBERT's code clone detection predictions.</div> <p>&nbsp;</p> <h2>Artifact Contents</h2> <h3>1. Core Implementation</h3> <div> <ul> <li>&nbsp;GraphCodeBERT_CloneDetection.ipynb: Complete Jupyter notebook containing: <ul> <li>GraphCodeBERT model setup and training</li> <li>Code clone detection experiments on BigCloneBench and Google Code Jam datasets</li> <li>In-Context Learning prompt generation for explanation</li> <li>LLM-based explanation pipeline</li> </ul> </li> </ul> </div> <h3>2. In-Context Learning Prompts (ICL_Prompts)</h3> <div>The ICL_Prompts directory contains structured prompts for 10 different Google Code Jam pairs (data_GoogleCodeJam_Pair1 through data_GoogleCodeJam_Pair10) used in the manual validation step, each with varying context lengths:</div> <ul> <li>layer_size4.txt: prompts with 4 examples</li> <li>layer_size8.txt: prompts with 8 examples</li> <li>layer_size16.txt: prompts with 16 examples</li> <li>layer_size32.txt: prompts with 32 examples</li> <li>layer_size48.txt: prompts with 48 examples</li> <li>layer_size64.txt: prompts with 64 examples</li> </ul> <div>Each prompt file is based on the prompt template structure:</div> <ul> <li><strong>Context:</strong> Description of GraphCodeBERT model</li> <li><strong>Dataset:</strong> Examples with code pairs, confidence scores, and predictions</li> <li><strong>Question:</strong> A query asking for explanation of a specific code pair</li> <li><strong>Instructions</strong> for generating explanations</li> </ul> <h3>3. Validation Results</h3> <div> <ul> <li>Manual_Validation_Results.xlsx: Manual evaluation results of generated explanations including quality assessments and human annotations.</li> </ul> </div> <h2>Usage Instructions</h2> <h3>Prerequisites</h3> <div><code>pip install torch transformers tree_sitter scikit-learn</code></div> <div>&nbsp;</div> <h3>Running the Code</h3> <ol> <li>Open `GraphCodeBERT_CloneDetection.ipynb` in Jupyter/Colab</li> <li>Follow the notebook cells to: <ol> <li>Set up the GraphCodeBERT model</li> <li>Load and preprocess datasets</li> <li>Run clone detection experiments</li> <li>Generate prompts for explanation</li> </ol> </li> </ol> <h3>File Organization</h3> <div><code>├── GraphCodeBERT_CloneDetection.ipynb # Main implementation</code></div> <div><code>├── Manual_Validation_Results.xlsx # Human evaluation results</code></div> <div><code>├── ICL_Prompts/ # Generated prompts</code></div> <div><code>│ ├── data_GoogleCodeJam_Pair1/ # Pair 1 prompts</code></div> <div><code>│ │ ├── layer_size4.txt # 4-example prompts</code></div> <div><code>│ │ ├── layer_size8.txt # 8-example prompts</code></div> <div><code>│ │ └── ... # Other sizes</code></div> <div><code>│ ├── data_GoogleCodeJam_Pair2/ # Pair 2 prompts</code></div> <div><code>│ └── ... # Additional pairs</code></div> <div><code>└── README.md # This file</code></div> <h3>Citation</h3> <div>Please cite this artefact using the DOI provided by Zenodo.</div> <h3>Contact</h3> <div>For questions about this artifact or research, please contact the authors [to be updated due to double-blind policy].</div>

opencc-by-4.0Jun 2024View details →
ClinicalTrials.gov32/100

PREVALENCE STUDY OF PNH CLONES IN PATIENTS WITH NEOPLASIES

ClinicalTrials.gov study NCT06159816. IPD Sharing: Not stated. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

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