cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10574330
title: Towards Explainable Classification of Non-Functional Requirements Using Fine-Tune-Chain-of-Thought Reasoning

description: Supplementary material for Towards Explainable Classification of Non-Functional Requirements Using Fine-Tune-Chain-of-Thought Reasoning 

Fine-tuned model

fine-tuned-flan-t5-base-nfr-identification-> Fine-tuned flan-t5-base model over 5 epochs for NFR identification

fine-tuned-flan-t5-large-nfr-identification> Fine-tuned flan-t5-large model over 3 epochs for NFR identification

fine-tuned-flan-t5-base-nfr-multilabel-classification -> Fine-tuned flan-t5-base model over 6 epochs for NFR classification

fine-tuned-flan-t5-large-nfr-multilabel-classification-> Fine-tuned flan-t5-large model over 3 epochs for NFR classification

 

Structure of artifacts.zip



1. Code

    1. fine_tuning.py - This script is used for fine-tuning the classifiers. The same script works for both nfr identification and nfr classification (for training separate models).

    2. inference.py - This script makes predictions using the finetuned models. It predicts on the datasets PURE-nfr-identification-data (level1).xlsx, PURE-nfr-identification-data (level1).xlsx, and PURE-nfr-classification-data (level2).xlsx in testind_dataset folder.




 

2. training_data

    1. promise-exp-nfr-classification-data.xlsx - For training NFR classification model; Annotated in a multilabel classification scheme.

    2. promise-exp-nfr-identification-data.xlsx - For training NFR identification model; Annotated in a multilabel classification scheme (FR, NFR, FR+NFR, None).


    Both of these files also contain the few-shot generated output of gpt-3.5




 

3. testing_data

    1. EHR_nfr_identification (level 1).xlsx - Electronics Health Records dataset; Inference ran using fine-tuned flan-t5-large for NFR identification.

    2. PURE-nfr-identification-data (level1).xlsx - PURE dataset with requirements annotated in a multilabel classification scheme (FR, NFR, FR+NFR, None); Inference ran using fine-tuned flan-t5-large and flan-t5-base for NFR identification.

    3. PURE-nfr-classification-data (level2).xlsx - PURE dataset with NFRs annotated in a multilabel classification scheme.; Inference ran using fine-tuned flan-t5-large and flan-t5-base for NFR classification.

 

 

Version 2 of this repository contains the llama generated output for NFR identification on level 1. Here is the link to version 2 > https://zenodo.org/records/10598270
DOI: 10.25919/byjw-v161
title: Hand-eye calibration of 2D laser profiler

description: Video showing the process of performing hand-eye calibration process.
DOI: 10.6084/m9.figshare.24548008.v4
title: <b>CO</b><sub><strong>2</strong></sub><b> </b><b>emissions from global on-road vehicles by vehicle- and fuel- type for each country during 1970-2020</b>

description: The data is structured as a tabular data including two sheets: CO<sub>2</sub> emissions data is in 'CO2' sheet, definitions of attributes in the data are in 'readme' sheet.<br>
DOI: 10.5281/zenodo.10118829
title: Origon date and video
DOI: 10.25442/hku.25444036
title: Supporting Data for journal article entitled "Hydrologic and Geological Controls on Chemical Weathering and Associated Carbon Sink in a Silicate-dominated River Basin"

description: This is the supporting data for journal article entitled "Hydrologic and Geological Controls on Chemical Weathering and Associated Carbon Sink in a Silicate-dominated River Basin". In this study, we aim to investigate the chemical weathering rate and weathering-induced carbon sink in the East River basin (ERB) by employing a forward model method to analyze river water chemistry. Water samples were collected during five fieldwork campaigns from December 2018 to October 2019, including three in the wet season and two in the dry season. In total, 43 sampling sites widely distributed across the ERB were visited during each campaign.This dataset includes the results from water chemistry analyses conducted at these sites.<br>
DOI: 10.25442/hku.25444036.v1
title: Supporting Data for journal article entitled "Hydrologic and Geological Controls on Chemical Weathering and Associated Carbon Sink in a Silicate-dominated River Basin"

description: This is the supporting data for journal article entitled "Hydrologic and Geological Controls on Chemical Weathering and Associated Carbon Sink in a Silicate-dominated River Basin". In this study, we aim to investigate the chemical weathering rate and weathering-induced carbon sink in the East River basin (ERB) by employing a forward model method to analyze river water chemistry. Water samples were collected during five fieldwork campaigns from December 2018 to October 2019, including three in the wet season and two in the dry season. In total, 43 sampling sites widely distributed across the ERB were visited during each campaign.This dataset includes the results from water chemistry analyses conducted at these sites.<br>
DOI: 10.5517/ccdc.csd.cc24wyll
title: CCDC 1993070: Experimental Crystal Structure Determination

description: Related Article: Xing Peng, Shaonan Liu, Yuting Zhang, Jun Xu, Qiong Gu|2024|Bioorg.Chem.|145|107253|doi:10.1016/j.bioorg.2024.107253
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc24wynn
title: CCDC 1993072: Experimental Crystal Structure Determination

description: Related Article: Xing Peng, Shaonan Liu, Yuting Zhang, Jun Xu, Qiong Gu|2024|Bioorg.Chem.|145|107253|doi:10.1016/j.bioorg.2024.107253
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.10118830
title: Origon date and video
DOI: 10.6084/m9.figshare.25296211.v1
title: 原始data.xlsx

description: Waste sorting
DOI: 10.5519/qd.691phq4i
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1393929 records)
DOI: 10.6084/m9.figshare.1399208.v16
title: Destabilization of pluripotency in the absence of Mad2l2

description: The induction and maintenance of pluripotency requires the expression of several core factors at appropriate levels (Oct4, Sox2, Klf4, Prdm14). A subset of these proteins (Oct4, Sox2, Prdm14) also plays crucial roles for the establishment of primordial germ cells (PGCs). Here we demonstrate that the Mad2l2 (MAD2B, Rev7) gene product is not only required by PGCs, but also by pluripotent embryonic stem cells (ESCs), depending on the growth conditions. Mad2l2<sup>−/−</sup> ESCs were unstable in LIF/serum medium, and differentiated into primitive endoderm. However, they could be stably propagated using small molecule inhibitors of MAPK signaling. Several components of the MAPK cascade were up- or downregulated even in undifferentiated Mad2l2<sup>−/−</sup> ESCs. Global levels of repressive histone H3 variants were increased in mutant ESCs, and the epigenetic signatures on pluripotency-, primitive endoderm-, and MAPK-related loci differed. Thus, H3K9me2 repressed the Nanog promoter, while the promoter of Gata4 lost H3K27me3 and became de-repressed in LIF/serum condition. Promoters associated with genes involved in MAPK signaling also showed misregulation of these histone marks. Such epigenetic modifications could be indirect consequences of mutating Mad2l2. However, our previous observations suggested the histone methyltransferases as direct (G9a) or indirect (Ezh2) targets of Mad2l2. In effect, the intricate balance necessary for pluripotency becomes perturbed in the absence of Mad2l2.
DOI: 10.6084/m9.figshare.1340078
title: Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt;3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1340078.v17
title: Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt;3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1399208
title: Destabilization of pluripotency in the absence of Mad2l2

description: The induction and maintenance of pluripotency requires the expression of several core factors at appropriate levels (Oct4, Sox2, Klf4, Prdm14). A subset of these proteins (Oct4, Sox2, Prdm14) also plays crucial roles for the establishment of primordial germ cells (PGCs). Here we demonstrate that the Mad2l2 (MAD2B, Rev7) gene product is not only required by PGCs, but also by pluripotent embryonic stem cells (ESCs), depending on the growth conditions. Mad2l2<sup>−/−</sup> ESCs were unstable in LIF/serum medium, and differentiated into primitive endoderm. However, they could be stably propagated using small molecule inhibitors of MAPK signaling. Several components of the MAPK cascade were up- or downregulated even in undifferentiated Mad2l2<sup>−/−</sup> ESCs. Global levels of repressive histone H3 variants were increased in mutant ESCs, and the epigenetic signatures on pluripotency-, primitive endoderm-, and MAPK-related loci differed. Thus, H3K9me2 repressed the Nanog promoter, while the promoter of Gata4 lost H3K27me3 and became de-repressed in LIF/serum condition. Promoters associated with genes involved in MAPK signaling also showed misregulation of these histone marks. Such epigenetic modifications could be indirect consequences of mutating Mad2l2. However, our previous observations suggested the histone methyltransferases as direct (G9a) or indirect (Ezh2) targets of Mad2l2. In effect, the intricate balance necessary for pluripotency becomes perturbed in the absence of Mad2l2.
DOI: 10.6084/m9.figshare.12601411
title: Phosphorylation-dependent degradation of MEF2C contributes to regulate G2/M transition

description: The Myocyte Enhancer Factor 2C (MEF2C) transcription factor plays a critical role in skeletal muscle differentiation, promoting muscle-specific gene transcription. Here we report that in proliferating cells MEF2C is degraded in mitosis by the Anaphase Promoting Complex/Cyclosome (APC/C) and that this downregulation is necessary for an efficient progression of the cell cycle. We show that this mechanism of degradation requires the presence on MEF2C of a D-box (R-<i>X-X</i>-L) and 2 phospho-motifs, pSer98 and pSer110. Both the D-box and pSer110 motifs are encoded by the ubiquitous alternate α1 exon. These two domains mediate the interaction between MEF2C and CDC20, a co-activator of APC/C. We further report that in myoblasts, MEF2C regulates the expression of G2/M checkpoint genes (<i>14–3–3</i>γ<i>, Gadd45b</i> and <i>p21</i>) and the sub-cellular localization of CYCLIN B1. The importance of controlling MEF2C levels during the cell cycle is reinforced by the observation that modulation of its expression affects the proliferation rate of colon cancer cells. Our findings show that beside the well-established role as pro-myogenic transcription factor, MEF2C can also function as a regulator of cell proliferation.
DOI: 10.6084/m9.figshare.12601411.v3
title: Phosphorylation-dependent degradation of MEF2C contributes to regulate G2/M transition

description: The Myocyte Enhancer Factor 2C (MEF2C) transcription factor plays a critical role in skeletal muscle differentiation, promoting muscle-specific gene transcription. Here we report that in proliferating cells MEF2C is degraded in mitosis by the Anaphase Promoting Complex/Cyclosome (APC/C) and that this downregulation is necessary for an efficient progression of the cell cycle. We show that this mechanism of degradation requires the presence on MEF2C of a D-box (R-<i>X-X</i>-L) and 2 phospho-motifs, pSer98 and pSer110. Both the D-box and pSer110 motifs are encoded by the ubiquitous alternate α1 exon. These two domains mediate the interaction between MEF2C and CDC20, a co-activator of APC/C. We further report that in myoblasts, MEF2C regulates the expression of G2/M checkpoint genes (<i>14–3–3</i>γ<i>, Gadd45b</i> and <i>p21</i>) and the sub-cellular localization of CYCLIN B1. The importance of controlling MEF2C levels during the cell cycle is reinforced by the observation that modulation of its expression affects the proliferation rate of colon cancer cells. Our findings show that beside the well-established role as pro-myogenic transcription factor, MEF2C can also function as a regulator of cell proliferation.
DOI: 10.6084/m9.figshare.25323121
title: Genome annotations of six Rhizophoraceae species

description: The genome assembly sequences and raw Illumina reads have been deposited in the NCBI with BioProject number PRJNA996495.The abbreviations of species names are as follows:<i>Carallia pectinifolia</i>: cape; <i>Ceriops tagal</i>: ceta; <i>Ceriops zippeliana</i>: cezi; <i>Kandelia candel</i>: kaca; <i>Rhizophora apiculata</i>: rhap; <i>Rhizophora mangle</i>: rhma.
DOI: 10.5066/p144puja
title: Vesicularity, grain size, and grain shape of basaltic pyroclasts from Kīlauea and Mauna Loa volcanoes, Island of Hawaiʻi

description: This dataset includes sample information, vesicularity by pycnometer, grain size and shape data by CAMSIZER, and measurements of crushed and thin section mounted grains by microscope. All studied samples were from scoria and air-fall-tephra deposits (most formed in Hawaiian lava fountains) collected around the summits of Mauna Loa and Kīlauea volcanoes, Island of Hawaiʻi. These data were used to derive methods for quickly being able to quantify vesicularity in near-real-time during an eruption response.

The samples from Kīlauea all erupted from the summit area and include Keanakākoʻi units B, D, E, K1, and K2, the Halemaʻumaʻu eruptions in September 2021 and September 2023, and the Kīlauea Iki eruption that formed the Puʻupuaʻi scoria cone. A single sample from the summit of Mauna Loa from the 1949 scoria cone was also used for this study.
DOI: 10.6084/m9.figshare.25458145
title: raw data files.xlsx

description: <b>Mitigation of Acute Lung Injury by Human Bronchial Epithelial Cell-derived Extracellular Vesicles via ANXA1-mediated FPR Signaling</b>
DOI: 10.7910/dvn/2sejda
title: Replication Data for: Addressing Risk by Doing Good: Business Response to Government Policy Initiative

description: Replication Data for: Addressing Risk by Doing Good: Business Response to Government Policy Initiative
DOI: 10.25345/c5pr7n53h
title: MassIVE MSV000094377 - Selective lipid recruitment by an archaeal DPANN symbiont from its host
title: Mass spectra data for 'Selective lipid recruitment by an archaeal DPANN symbiont from its host'. Su Ding*, Joshua N. Hamm*, Nicole J. Bale, Jaap S. Sinninghe Damste, Anja Spang doi: https://doi.org/10.1101/2023.12.06.570485
DOI: 10.6084/m9.figshare.25458127
title: DATABASE.xlsx

description: Database of the questionnaires applied to employees of the Peruvian retail sector.
DOI: 10.6084/m9.figshare.21603033.v11
title: Inhibition of mitochondrial complex III or dihydroorotate dehydrogenase (DHODH) triggers formation of poly(A)<sup>+</sup> RNA foci adjacent to nuclear speckles following activation of ATM (ataxia telangiectasia mutated)

description: Intracellular and intercellular signalling networks play an essential role in optimizing cellular homoeostasis and are thought to be partly reflected in nuclear mRNA dynamics. However, the regulation of nuclear mRNA dynamics by intracellular and intercellular signals remains largely unexplored, and research tools are lacking. Through an original screening based on the mRNA metabolic mechanism, we discovered that eight well-known inhibitors cause significant nuclear poly(A)<sup>+</sup> RNA accumulation. Among these inhibitors, we discovered a new mRNA metabolic response in which the addition of antimycin A, an inhibitor of mitochondrial respiratory-chain complex III (complex III), resulted in a marked accumulation of poly(A)<sup>+</sup> RNA near the nuclear speckles. Furthermore, dihydroorotate dehydrogenase (DHODH) inhibitors, a rate-limiting enzyme in the intracellular <i>de novo</i> pyrimidine synthesis reaction that specifically exchanges electrons with complex III, also caused a remarkable accumulation of nuclear poly(A)<sup>+</sup> RNA adjacent to the nuclear speckles, which was abolished by extracellular uridine supply, indicating that the depletion of intracellular pyrimidine affects poly(A)<sup>+</sup> RNA metabolism. Further analysis revealed that ataxia telangiectasia mutated (ATM), a serine and threonine kinase and a master regulator of DNA double-strand break (DSB) and nucleolar stress, is required for this poly(A)<sup>+</sup> RNA nuclear accumulation phenomenon. This study reports new insights into novel aspects of nuclear poly(A)<sup>+</sup> RNA metabolism, especially the relationship between mitochondrial respiratory-chain functions, pyrimidine metabolism, and nuclear RNA metabolism.
DOI: 10.5281/zenodo.10851241
title: Uranium isotope constraints on the pre-deposition time of Asian dust to the North Pacific Ocean: Implications for provenance and iron supply

description: This dataset presents uranium isotope data covering a 300,000-year period retrieved from Ocean Drilling Program site 1209B in the North Pacific Ocean. Additionally, it incorporates uranium-neodymium isotope data sourced from multiple deserts in China, providing a comprehensive reexamination of the origin of dust in the North Pacific region.
DOI: 10.5281/zenodo.10851243
title: Uranium isotope constraints on the pre-deposition time of Asian dust to the North Pacific Ocean: Implications for provenance and iron supply

description: This dataset presents uranium isotope data covering a 300,000-year period retrieved from Ocean Drilling Program site 1209B in the North Pacific Ocean. Additionally, it incorporates uranium-neodymium isotope data sourced from multiple deserts in China, providing a comprehensive reexamination of the origin of dust in the North Pacific region.
DOI: 10.5281/zenodo.10346758
title: Uranium isotope constraints on the transport time of Asian dust to the North Pacific Ocean: Implication for provenance and iron supply

description: This dataset presents uranium isotope data covering a 300,000-year period retrieved from Ocean Drilling Program site 1209B in the North Pacific Ocean. Additionally, it incorporates uranium-neodymium isotope data sourced from multiple deserts in China, providing a comprehensive reexamination of the origin of dust in the North Pacific region.
DOI: 10.23719/1530330
title: Benton Harbor Water Study Data

description: This dataset represents all of the data collected by EPA during the Benton Harbor Drinking Water Study, which was published as an EPA report: Tully, J., S. Shilling, V. Bosscher, M. Schock, and D. Lytle. Benton Harbor Drinking Water Study. U.S. Environmental Protection Agency, Washington, DC, USA, 2023.
For the journal article: An evaluation of properly operated NSF/ANSI-53 Pb certified drinking water filters in Benton Harbor, MI, published in 2024 (https://doi.org/10.2166/wh.2024.231). A subset of the filter study data, background water quality data, and particulate sample data was evaluated.