cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22671607.v1
title: Supplementary Material for: Prognostic Value of SSTR-derived Volumetric Parameters from a Hybrid Standardized Uptake Value Thresholding Method in Patients with 68Ga-DOTATATE-avid Stage IV Neuroendocrine Neoplasms: A preliminary study

description: Introduction: The ability of PET/CT imaging to delineate neuroendocrine neoplasms (NENs) and predict prognosis in affected patients is often compromised by substantial uptake heterogeneity. We hereby proposed a hybrid standardized uptake value (SUV) thresholding algorithm to extract volumetric parameters from somatostatin receptor (SSTR) PET/CT imaging, and investigate their prognostic performance in patients with 68Ga-DOTATATE-avid stage IV NENs. Methods: For 38 retrospectively enrolled patients, we used either fixed SUV thresholding of normal liver parenchyma (method A), 41% of the SUVmax for each lesion (method B), or a hybrid method (method A for liver metastases; fixed SUV threshold of normal bone for bone metastases; method B for primary tumors and other metastases) to quantify the whole-body SSTR-expressing tumor volume (SRETVwb) and total lesion SSTR expression (TLSREwb). Patient survival was also recorded and analyzed. Results: PET/CT images revealed heterogeneous uptake of 68Ga-DOTATATE at primary and metastatic sites. Progression-free (PFS) and overall survival (OS) were negatively correlated with the extent of liver or bone metastases (P &lt; 0.05), but not significantly correlated with tumor grade or 18F-FDG PET/CT positivity. By the hybrid method, PFS was significantly shorter in patients with high SRETVwb, and OS was significantly shorter in those with high SRETVwb and TLSREwb (P &lt; 0.05). However, when derived from method A or method B, neither SRETVwb nor TLSREwb could predict patient outcomes. Conclusion: Compared with other methods used in 68Ga-DOTATATE-avid stage IV NENs, our hybrid SUV thresholding method demonstrated robustness, with greater precision, reliability, and prognostic power.
DOI: 10.34740/kaggle/dsv/5920391
title: 2021 World Population (updated daily)
DOI: 10.5281/zenodo.7189293
title: CESNET-MINER22

description: <strong>CESNET-MINER22 : Datasets of Cryptomining Communication</strong> This dataset was created to design a detector of cryptominers communication, soon to be published in NordSec 2022 - IT security conference: Plný, R.; Hynek, K.; Čejka; T.: DeCrypto: Finding Cryptocurrency Miners on ISP networks, in Proceedings of the 27th Nordic Conference on Secure IT Systems, 2022. File named <code>decrypto_dataset_design.csv</code> contains 2,024,903 anonymized flows collected on the national CESNET2 network from December 2021 to February 2022. File named <code>decrypto_dataset_evaluation.csv</code> contains of 1,075,576 anonymized flows collected on the national CESNET2 network during March 2022. Both datasets are provided in CSV format and were created by ipfixprobe. See field description provided below. <strong>BYTES</strong> Number of transferred bytes (from client to server). <strong>BYTES_REV</strong> Number of transferred bytes in the opposite direction (from server to client). <strong>DST_PORT</strong> Destination port. <strong>LABEL</strong> Flow label. Possible values are: Miner Other <strong>PACKETS</strong> Number of transferred packets (from client to server). <strong>PACKETS_REV</strong> Number of transferred packets in the opposite direction (from server to client). <strong>PPI_PKT_DIRECTIONS</strong> Array of directions of the first 30 packets. Values: 1 represents direction client-&gt;server -1 represents direction server-&gt;client. <strong>PPI_PKT_FLAGS</strong> Array of TCP flags of the first 30 packets. <strong>PPI_PKT_LENGTHS</strong> Array of packet sizes of the first 30 packets. <strong>PPI_PKT_TIMES</strong> Array of timestamps of intercept of the first 30 packets. <strong>PROTOCOL</strong> Used protocol on the Transport layer of the ISO/OSI. TCP is represented by the value 6. <strong>SRC_PORT</strong> Source port. <strong>TCP_FLAGS</strong> TCP flags of the first packet (sent by client). <strong>TCP_FLAGS_REV</strong> TCP flags of the first packer from the opposite direction (sent by server). <strong>TIME_FIRST</strong> Time of interception of the first packet in the flow. <strong>TIME_LAST</strong> Time of interception of the last packet in the flow.
description: Acknowledgements This research was funded by the Ministry of Interior of the Czech Republic, grant No. VJ02010024: Flow-Based Encrypted Traffic Analysis and also by the Grant Agency of the CTU in Prague, grant No. SGS20/210/OHK3/3T/18 funded by the MEYS of the Czech Republic.
DOI: 10.5281/zenodo.7189292
title: CESNET-MINER22

description: <strong>CESNET-MINER22 : Datasets of Cryptomining Communication</strong> This dataset was created to design a detector of cryptominers communication, soon to be published in NordSec 2022 - IT security conference: Plný, R.; Hynek, K.; Čejka; T.: DeCrypto: Finding Cryptocurrency Miners on ISP networks, in Proceedings of the 27th Nordic Conference on Secure IT Systems, 2022. File named <code>decrypto_dataset_design.csv</code> contains 2,024,903 anonymized flows collected on the national CESNET2 network from December 2021 to February 2022. File named <code>decrypto_dataset_evaluation.csv</code> contains of 1,075,576 anonymized flows collected on the national CESNET2 network during March 2022. Both datasets are provided in CSV format and were created by ipfixprobe. See field description provided below. <strong>BYTES</strong> Number of transferred bytes (from client to server). <strong>BYTES_REV</strong> Number of transferred bytes in the opposite direction (from server to client). <strong>DST_PORT</strong> Destination port. <strong>LABEL</strong> Flow label. Possible values are: Miner Other <strong>PACKETS</strong> Number of transferred packets (from client to server). <strong>PACKETS_REV</strong> Number of transferred packets in the opposite direction (from server to client). <strong>PPI_PKT_DIRECTIONS</strong> Array of directions of the first 30 packets. Values: 1 represents direction client-&gt;server -1 represents direction server-&gt;client. <strong>PPI_PKT_FLAGS</strong> Array of TCP flags of the first 30 packets. <strong>PPI_PKT_LENGTHS</strong> Array of packet sizes of the first 30 packets. <strong>PPI_PKT_TIMES</strong> Array of timestamps of intercept of the first 30 packets. <strong>PROTOCOL</strong> Used protocol on the Transport layer of the ISO/OSI. TCP is represented by the value 6. <strong>SRC_PORT</strong> Source port. <strong>TCP_FLAGS</strong> TCP flags of the first packet (sent by client). <strong>TCP_FLAGS_REV</strong> TCP flags of the first packer from the opposite direction (sent by server). <strong>TIME_FIRST</strong> Time of interception of the first packet in the flow. <strong>TIME_LAST</strong> Time of interception of the last packet in the flow.
description: Acknowledgements This research was funded by the Ministry of Interior of the Czech Republic, grant No. VJ02010024: Flow-Based Encrypted Traffic Analysis and also by the Grant Agency of the CTU in Prague, grant No. SGS20/210/OHK3/3T/18 funded by the MEYS of the Czech Republic.
DOI: 10.6069/vktp-ny17
title: Orthogonal proteomics methods warrants development of Duchenne Muscular Dystrophy biomarkers

description: Background:
Molecular components in blood, such as proteins, are used as biomarkers to detect or predict disease states, guide clinical interventions and aid in the development of therapies. While multiplexing proteomics methods promote discovery of such biomarkers, their translation to clinical use is difficult due to the lack of substantial evidence regarding their reliability as quantifiable indicators of disease state or outcome. To overcome this challenge, a novel orthogonal strategy was developed and used to assess the reliability of biomarkers and analytically corroborate already identified serum biomarkers for Duchenne muscular dystrophy (DMD). DMD is a monogenic incurable disease characterized by progressive muscle damage that currently lacks reliable and specific disease monitoring tools.

Methods:
Two technological platforms are used to detect and quantify the biomarkers in 72 longitudinally collected serum samples from DMD patients at 3 to 5 timepoints. Quantification of the biomarkers is achieved by detection of the same biomarker fragment either through interaction with validated antibodies in immuno-assays or through quantification of peptides by Parallel Reaction Monitoring Mass Spectrometry assay (PRM-MS).

Results
Five, out of ten biomarkers previously identified by affinity-based proteomics methods, were confirmed to be associated with DMD using the mass spectrometry-based method. Two biomarkers, carbonic anhydrase III and lactate dehydrogenase B, were quantified with two independent methods, sandwich immunoassays and PRM-MS, with Pearson correlations of 0.92 and 0.946 respectively. The median concentrations of CA3 and LDHB in DMD patients was elevated in comparison to those in healthy individuals by 35- and 3-fold, respectively. Levels of CA3 vary between 10.26 and 0.36 ng/ml in DMD patients whereas those of LDHB vary between 15.1 and 0.8 ng/ml.

Conclusions:
These results demonstrate that orthogonal assays can be used to assess the analytical reliability of biomarker quantification assays, providing a means to facilitate the translation of biomarkers to clinical practice. This strategy also warrants the development of the most relevant biomarkers, markers that can be reliably quantified with different proteomics methods.
DOI: 10.5281/zenodo.8033501
title: desmognathus_balsameus_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8033500
title: desmognathus_balsameus_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.7874912
title: Evaluating the Impact of Third-Party Library Reuse in Java Projects: An Empirical Study

description: This part of the submission related to the paper "Evaluating the Impact of Third-Party Library Reuse in Java Projects: An Empirical Study". Due to company review policies of code such as all processing scrips will be added once approval is reached. Here is a table of contents: `census.csv`: extracted data from the Census-II `releases_all.csv`: all releases available from Maven Coordinates in Census-II `releases_jar.csv`: dataset of all releases with a POM and JAR file `releases_jar_6_months.csv`: releases selected when studiying the 6-month interval `releases_jar_6_months.csv`: releases selected when comparing consecutive versions per artefactid and groupid `loc_composition.csv`: data on the ratio of insourced and outsourced code in project releases `loc_desc_without_lambdas.csv`: mined data on LOC information and class information. `loc_reuse_lower_bound.csv`: data on the ratio of reused LOC and functions of outsourced code, lower-bound `loc_reuse_upper_bound.csv`: data on the ratio of reused LOC and functions of outsourced code, upper-bound
DOI: 10.5281/zenodo.8033508
title: enteromius_thamalakanensis_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8033507
title: enteromius_thamalakanensis_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23508549
title: SI Appendix Table

description: SI Appendix Table
DOI: 10.6084/m9.figshare.23508549.v1
title: SI Appendix Table

description: SI Appendix Table
DOI: 10.5281/zenodo.8033511
title: sandelia_bainsii_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8033510
title: sandelia_bainsii_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.22852937
title: Minimal dataset for ConFindr testing using pytest

description: A .tar.gz archive containing 14 .fastq.gz files, which correspond to paired-end Illumina whole-genome sequence data from different foodborne pathogens, and an associated tab-separated value file for the metadata of these samples. These sequence data were obtained by selecting samples from the originally published ConFindr dataset (doi: 10.7717/peerj.6995) and downsampling them. The metadata for these samples was obtained from the Supplemental Information of the original publication. The DownsampleFactor column in the metadata file corresponds to the factor by which the original samples were downsampled (e.g. 0.5 is 2-fold downsampling, 0.1 is 10-fold). <br> Changelog <br> Version 3 <br> Changed test_samples archive from .zip to .tar.gz, as it was in Version 1. <br> Version 2 <br> Renamed '_1' and '_2' file patterns to '_R1' and '_R2' to reflect default ConFindr parameters.
DOI: 10.6084/m9.figshare.22852937.v2
title: Minimal dataset for ConFindr testing using pytest

description: A .tar.gz archive containing 14 .fastq.gz files, which correspond to paired-end Illumina whole-genome sequence data from different foodborne pathogens, and an associated tab-separated value file for the metadata of these samples. These sequence data were obtained by selecting samples from the originally published ConFindr dataset (doi: 10.7717/peerj.6995) and downsampling them. The metadata for these samples was obtained from the Supplemental Information of the original publication. The DownsampleFactor column in the metadata file corresponds to the factor by which the original samples were downsampled (e.g. 0.5 is 2-fold downsampling, 0.1 is 10-fold). <br> Changelog <br> 2023-06-13 <br> Renamed '_1' and '_2' file patterns to '_R1' and '_R2' to reflect default ConFindr parameters.
DOI: 10.6084/m9.figshare.20029415
title: Synthesis, structural characterization, DFT calculations, molecular docking, and molecular dynamics simulations of a novel ferrocene derivative to unravel its potential antitumor activity

description: In this article, we describe a set of subsequent five-steps chemical reactions to synthesize a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>). Structural characterization of <b>10</b> and its intermediate products was also performed and reported to attest to their formation. A molecular docking study was performed to propose the novel synthesized ferrocene derivative (<b>10</b>) as a potential antitumor candidate targeting the mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. The computed docking score of (<b>10</b>) at −9.50 kcal/mol compared to the native anticancer staurosporine at −8.72 kcal/mol postulated a promising anticancer activity. Also, molecular dynamics (MD) simulations were carried out for 500 ns followed by MM-GBSA-binding free energy calculations for both the docked complexes of ferrocene and staurosporine to give more deep insights into their dynamic behavior in physiological conditions. Furthermore, DFT calculations were performed to unravel some of the physiochemical characteristics of the ferrocene derivative (<b>10</b>). The quantum mechanics calculations shed the light on some of the structural and electrochemical configurations of (<b>10</b>) which would open the horizon for further investigation. HighlightsThe synthesis of a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>) was described.Structural characterizations of ferrocene derivative (<b>10</b>) and its intermediate products were also performed.DFT calculations, molecular docking, molecular dynamics, and MM-GBSA calculations were carried out.Computational studies revealed the antitumor potential of ferrocene derivative (<b>10</b>) through targeting and inhibiting mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. The synthesis of a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>) was described. Structural characterizations of ferrocene derivative (<b>10</b>) and its intermediate products were also performed. DFT calculations, molecular docking, molecular dynamics, and MM-GBSA calculations were carried out. Computational studies revealed the antitumor potential of ferrocene derivative (<b>10</b>) through targeting and inhibiting mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20029415.v2
title: Synthesis, structural characterization, DFT calculations, molecular docking, and molecular dynamics simulations of a novel ferrocene derivative to unravel its potential antitumor activity

description: In this article, we describe a set of subsequent five-steps chemical reactions to synthesize a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>). Structural characterization of <b>10</b> and its intermediate products was also performed and reported to attest to their formation. A molecular docking study was performed to propose the novel synthesized ferrocene derivative (<b>10</b>) as a potential antitumor candidate targeting the mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. The computed docking score of (<b>10</b>) at −9.50 kcal/mol compared to the native anticancer staurosporine at −8.72 kcal/mol postulated a promising anticancer activity. Also, molecular dynamics (MD) simulations were carried out for 500 ns followed by MM-GBSA-binding free energy calculations for both the docked complexes of ferrocene and staurosporine to give more deep insights into their dynamic behavior in physiological conditions. Furthermore, DFT calculations were performed to unravel some of the physiochemical characteristics of the ferrocene derivative (<b>10</b>). The quantum mechanics calculations shed the light on some of the structural and electrochemical configurations of (<b>10</b>) which would open the horizon for further investigation. HighlightsThe synthesis of a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>) was described.Structural characterizations of ferrocene derivative (<b>10</b>) and its intermediate products were also performed.DFT calculations, molecular docking, molecular dynamics, and MM-GBSA calculations were carried out.Computational studies revealed the antitumor potential of ferrocene derivative (<b>10</b>) through targeting and inhibiting mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. The synthesis of a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>) was described. Structural characterizations of ferrocene derivative (<b>10</b>) and its intermediate products were also performed. DFT calculations, molecular docking, molecular dynamics, and MM-GBSA calculations were carried out. Computational studies revealed the antitumor potential of ferrocene derivative (<b>10</b>) through targeting and inhibiting mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20029415.v1
title: Synthesis, structural characterization, DFT calculations, molecular docking, and molecular dynamics simulations of a novel ferrocene derivative to unravel its potential antitumor activity

description: In this article, we describe a set of subsequent five-steps chemical reactions to synthesize a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>). Structural characterization of <b>10</b> and its intermediate products was also performed and reported to attest to their formation. A molecular docking study was performed to propose the novel synthesized ferrocene derivative (<b>10</b>) as a potential antitumor candidate targeting the mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. The computed docking score of (<b>10</b>) at −9.50 kcal/mol compared to the native anticancer staurosporine at −8.72 kcal/mol postulated a promising anticancer activity. Also, molecular dynamics (MD) simulations were carried out for 500 ns followed by MM-GBSA-binding free energy calculations for both the docked complexes of ferrocene and staurosporine to give more deep insights into their dynamic behavior in physiological conditions. Furthermore, DFT calculations were performed to unravel some of the physiochemical characteristics of the ferrocene derivative (<b>10</b>). The quantum mechanics calculations shed the light on some of the structural and electrochemical configurations of (<b>10</b>) which would open the horizon for further investigation. HighlightsThe synthesis of a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>) was described.Structural characterizations of ferrocene derivative (<b>10</b>) and its intermediate products were also performed.DFT calculations, molecular docking, molecular dynamics, and MM-GBSA calculations were carried out.Computational studies revealed the antitumor potential of ferrocene derivative (<b>10</b>) through targeting and inhibiting mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. The synthesis of a ferrocene derivative named 1-(5-(diphenylphosphaneyl)cyclopenta-1,3-dien-1-yl)ethyl)imino)-1,3-dihydroisobenzofuran-5-yl)methanol (<b>compound 10</b>) was described. Structural characterizations of ferrocene derivative (<b>10</b>) and its intermediate products were also performed. DFT calculations, molecular docking, molecular dynamics, and MM-GBSA calculations were carried out. Computational studies revealed the antitumor potential of ferrocene derivative (<b>10</b>) through targeting and inhibiting mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.19780370.v1
title: <i>In silico</i> insights into the dimer structure and deiodinase activity of type III iodothyronine deiodinase from bioinformatics, molecular dynamics simulations, and QM/MM calculations

description: The homodimeric family of iodothyronine deiodinases (Dios) regioselectively remove iodine from thyroid hormones. Currently, structural data has only been reported for the monomer of the <i>mus</i> type III thioredoxin (Trx) fold catalytic domain (Dio3<sup>Trx</sup>), but the mode of dimerization has not yet been determined. Various groups have proposed dimer structures that are similar to the A-type and B-type dimerization modes of peroxiredoxins. Computational methods are used to compare the sequence of Dio3<sup>Trx</sup> to related proteins known to form A-type and B-type dimers. Sequence analysis and <i>in silico</i> protein-protein docking methods suggest that Dio3<sup>Trx</sup> is more consistent with proteins that adopt B-type dimerization. Molecular dynamics (MD) simulations of the refined Dio3<sup>Trx</sup> dimer constructed using the SymmDock and GalaxyRefineComplex databases indicate stable dimer formation along the β<sub>4</sub>α<sub>3</sub> interface consistent with other Trx fold B-type dimers. Free energy calculations show that the dimer is stabilized by interdimer interactions between the β-sheets and α-helices. A comparison of MD simulations of the <i>apo</i> and thyroxine-bound dimers suggests that the active site binding pocket is not affected by dimerization. Determination of the transition state for deiodination of thyroxine from the monomer structure using QM/MM methods provides an activation barrier consistent with previous small model DFT studies. Communicated by Ramaswamy H. Sarma