cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10259996
title: BIDS CHB-MIT Scalp EEG Database

description: This dataset is a BIDS-compatible version of the CHB-MIT Scalp EEG Database. It reorganizes the file structure to comply with the BIDS specification. To this effect:

The data from subject chb21 was moved to sub-01/ses-02.
Metadata was organized according to BIDS.
Data in the EEG edf files was modified to keep only the 18 channels from a double banana bipolar montage.
Annotations were formatted as BIDS-score compatible `tsv` files.
Details related to access to the data
License
The dataset is released under the Open Data Commons Attribution License v1.0.
Contact person
The original Physionet CHB-MIT Scalp EEG Database was published by Ali Shoeb. This BIDS-compatible version of the dataset was published by Jonathan Dan.
Practical information to access the data
The original Physionet CHB-MIT Scalp EEG Database is available on the Physionet website.
Overview
Project name
CHB-MIT Scalp EEG Database
Year that the project ran
2010
Brief overview of the tasks in the experiment
This database, collected at the Children's Hospital Boston, consists of EEG recordings from pediatric subjects with intractable seizures. Subjects were monitored for up to several days following withdrawal of anti-seizure medication in order to characterize their seizures and assess their candidacy for surgical intervention.
Description of the contents of the dataset
Each folder (sub-01, sub-01, etc.) contains between 9 and 42 continuous .edf files from a single subject. Hardware limitations resulted in gaps between consecutively-numbered .edf files, during which the signals were not recorded; in most cases, the gaps are 10 seconds or less, but occasionally there are much longer gaps. In order to protect the privacy of the subjects, all protected health information (PHI) in the original .edf files has been replaced with surrogate information in the files provided here. Dates in the original .edf files have been replaced by surrogate dates, but the time relationships between the individual files belonging to each case have been preserved. In most cases, the .edf files contain exactly one hour of digitized EEG signals, although those belonging to case sub-10 are two hours long, and those belonging to cases sub-04, sub-06, sub-07, sub-09, and sub-23 are four hours long; occasionally, files in which seizures are recorded are shorter.
The EEG is recorded at 256 Hz with a 16-bit resolution. The recordings are referenced in a double banana bipolar montage with 18 channels from the 10-20 electrode system.
The dataset also contains seizure annotations as start and stop times.
The dataset contains 664 `.edf` recordings. 129 those files that contain one or more seizures. In all, these records include 198 seizures.
Methods
Subjects
23 pediatric subjects with intractable seizures. (5 males, ages 3–22; and 17 females, ages 1.5–19; 1 n/a)
Apparatus
Recordings were performed at the Children's Hospital Boston using the International 10-20 system of EEG electrode positions. Signals were sampled at 256 samples per second with 16-bit resolution.
DOI: 10.6084/m9.figshare.24746103
title: Supplementary Material for: Effects of exclusive breastfeeding promotion interventions on child outcomes: a systematic review and meta-analysis

description: Introduction: Interventions promoting exclusive breastfeeding (EBF) may benefit infant health outcomes, but evidence is inconsistent. The objective of this review was to assess the effect of interventions promoting EBF on health outcomes in infants and children under 7 years of age. Methods: A literature search was conducted using EMBASE, MEDLINE, CINAHL, Cochrane Central, Cochrane Database of Systematic Reviews, and WHO International Clinical Trials Registry Platform from inception to April 2022. Inclusion criteria were randomized or cluster-randomized controlled trials aiming to increase EBF that reported effects on offspring growth, morbidity and/or mortality up to age 7 years. The primary outcome was infant/child growth. Secondary outcomes were infant morbidity and mortality and exclusive breastfeeding rates. Data were pooled using a random-effects model. Results: 32 studies (40 papers) were identified. No effect on infant/child growth was observed. EBF promotion interventions significantly improved EBF rates up to 6 months (n=25; OR 3.15; 95%CI 2.36,4.19) and significantly reduced the odds of respiratory illness at 0-3 months by 59% (n=2; OR 0.41; 95%CI 0.20,0.84) but not at later time-points. A borderline significant effect was observed for diarrhea (n=12; OR 0.84; 95%CI 0.70,1.00). Effects on hospitalizations or mortality were not significant. Discussion/Conclusion: EBF promotion interventions improve EBF rates and might yield modest reductions in infant morbidity without affecting infant/child growth. Future studies should investigate the cost-effectiveness of these interventions and examine potential benefits on other health outcomes.
DOI: 10.20387/bonares-j4tw-7a9h
title: Agroclimatic indicators data of Long-Term Field Experiments in Germany - BIOCLIMATIC INDICATORS

description: This dataset was employed in our study titled "Climate change effects on long-term field experiments in Germany," which can be accessed with the following DOI: https://doi.org/10.1016/j.agsy.2022.103578. The dataset encompassed climate data for both the baseline period (1970-2000) and future projections (extending up to 2100), sourced from the WorldClim database (Worldclim, 2021) for the European region, with a spatial resolution of 2.5 minutes (approximately 5 kilometers). This dataset was generated as part of the Coupled Model Intercomparison Project Phase 6 (CMIP6) and included monthly records of minimum temperature, maximum temperature, and precipitation from nine global climate models (GCMs) spanning up to the year 2100. We employed the average data derived from these GCMs, incorporating data averaged over four 20-year intervals (2021–2040, 2041–2060, 2061–2080, 2081–2100). These future climate projections for Germany were based on four emission scenarios, namely SSP126, SSP245, SSP370, and SSP585.
This table contains data on - BIOCLIMATIC INDICATORS



Related datasets are listed in the metadata element 'Related Identifier'.
Dataset version 1.0
DOI: 10.6084/m9.figshare.24745335
title: Alcohol reduces choosiness and relaxes mate preferences in female <i>Drosophila simulans</i>

description: Here are the data and R code for the manuscript "Alcohol reduces choosiness and relaxes mate preferences in female <i>Drosophila simulans."</i>If you have any questions, please feel free to email rutharcher0 - at - gmail.com<br>
DOI: 10.6084/m9.figshare.24745335.v1
title: Alcohol reduces choosiness and relaxes mate preferences in female <i>Drosophila simulans</i>

description: Here are the data and R code for the manuscript "Alcohol reduces choosiness and relaxes mate preferences in female <i>Drosophila simulans."</i>If you have any questions, please feel free to email rutharcher0 - at - gmail.com<br>
DOI: 10.57967/hf/1424
title: OPC_UA_NER_BC
DOI: 10.6084/m9.figshare.24647532.v4
title: criminal-charge-in-taiwan.csv

description: This dataset is used for NLP research and primarily collects criminal judgment cases from Taiwan district courts from January 2020 to April 2022.
DOI: 10.6084/m9.figshare.24647532.v5
title: criminal-charge-in-taiwan.csv

description: This dataset is used for NLP research and primarily collects criminal judgment cases from Taiwan district courts from January 2020 to April 2022.
DOI: 10.34740/kaggle/dsv/7129285
title: 2021 World Population (updated daily)
DOI: 10.6084/m9.figshare.24586441
title: GXMR-CAR containing distinct GXM-specific single-chain variable fragment (scFv) mediated the cell activation against <i>Cryptococcus</i> spp. And had difference in the strength of tonic signaling

description: <i>Cryptococcus</i> spp. has a polysaccharide capsule composed of glucuronoxylomannan-GXM, a major virulence factor that can prevent the recognition of fungi by immune cells. Chimeric Antigen Receptor (CAR) redirects T cells to target <i>Cryptococcus</i> spp. as previously demonstrated by a CAR specific to GXM, GXMR-CAR. The current study evaluated the strength of the signal transduction triggered by GXMR-CAR, composed of a distinct antigen-binding domain sourced from a single-chain variable fragment (scFv). GXM-specific scFv derived from mAbs 2H1 and 18B7, 2H1-GXMR-CAR and 18B7-GXMR-CAR, respectively, were designed to express CD8 molecule as hinge/transmembrane, and the costimulatory molecule CD137 (4-1BB) coupled to CD3ζ. The 2H1-GXMR-CAR or 18B7-GXMR-CAR Jurkat cells recognized soluble GXM from C. gattii and C. neoformans, and the levels of IL-2 released by the modified cells did not differ between the GXMR-CAR constructs after exposure to <i>Cryptococcus</i> spp. 18B7-GXMR-CAR triggered tonic signaling was more pronounced in modified Jurkat cells, and a protein kinase inhibitor of the Src family (dasatinib) significantly reduced GXMR-CAR tonic signaling and inhibited cell activation against ligands. 18B7 scFv showed a structural modification of the variable heavy (VH) chain that clarified the difference in the strength of tonic signaling and the level of cell activation between 2H1-GXMR-CAR and 18B7-GXMR-CAR. GXMR-CAR constructs induced T-cell activation against clinical isolates of <i>Cryptococcus</i> spp. and serum from patients with cryptococcosis induced high levels of IL-2, mainly in cells modified with 18B7-GXMR-CAR. Thus, 18B7-GXMR-CAR and 2H1-GXMR-CAR mediated T cell activation against Cryptococcus spp. and 18B7 and 2H1 scFv influenced the strength of tonic signaling. 2H1-GXMR-CAR and 18B7-GXMR-CAR are efficiently expressed on the cell surface;2H1-GXMR-CAR and 18B7-GXMR-CAR redirected T cells toward the ligands;18B7-GXMR-CAR provided highest levels of tonic signaling;Binding pocket of 18B7 scFv favored the tonic signaling triggered by GXMR-CAR;Binding pocket of 18B7 scFv favored the tonic signaling triggered by GXMR-CAR; 2H1-GXMR-CAR and 18B7-GXMR-CAR are efficiently expressed on the cell surface; 2H1-GXMR-CAR and 18B7-GXMR-CAR redirected T cells toward the ligands; 18B7-GXMR-CAR provided highest levels of tonic signaling; Binding pocket of 18B7 scFv favored the tonic signaling triggered by GXMR-CAR; Binding pocket of 18B7 scFv favored the tonic signaling triggered by GXMR-CAR;
DOI: 10.6084/m9.figshare.24586441.v1
title: GXMR-CAR containing distinct GXM-specific single-chain variable fragment (scFv) mediated the cell activation against <i>Cryptococcus</i> spp. And had difference in the strength of tonic signaling

description: <i>Cryptococcus</i> spp. has a polysaccharide capsule composed of glucuronoxylomannan-GXM, a major virulence factor that can prevent the recognition of fungi by immune cells. Chimeric Antigen Receptor (CAR) redirects T cells to target <i>Cryptococcus</i> spp. as previously demonstrated by a CAR specific to GXM, GXMR-CAR. The current study evaluated the strength of the signal transduction triggered by GXMR-CAR, composed of a distinct antigen-binding domain sourced from a single-chain variable fragment (scFv). GXM-specific scFv derived from mAbs 2H1 and 18B7, 2H1-GXMR-CAR and 18B7-GXMR-CAR, respectively, were designed to express CD8 molecule as hinge/transmembrane, and the costimulatory molecule CD137 (4-1BB) coupled to CD3ζ. The 2H1-GXMR-CAR or 18B7-GXMR-CAR Jurkat cells recognized soluble GXM from C. gattii and C. neoformans, and the levels of IL-2 released by the modified cells did not differ between the GXMR-CAR constructs after exposure to <i>Cryptococcus</i> spp. 18B7-GXMR-CAR triggered tonic signaling was more pronounced in modified Jurkat cells, and a protein kinase inhibitor of the Src family (dasatinib) significantly reduced GXMR-CAR tonic signaling and inhibited cell activation against ligands. 18B7 scFv showed a structural modification of the variable heavy (VH) chain that clarified the difference in the strength of tonic signaling and the level of cell activation between 2H1-GXMR-CAR and 18B7-GXMR-CAR. GXMR-CAR constructs induced T-cell activation against clinical isolates of <i>Cryptococcus</i> spp. and serum from patients with cryptococcosis induced high levels of IL-2, mainly in cells modified with 18B7-GXMR-CAR. Thus, 18B7-GXMR-CAR and 2H1-GXMR-CAR mediated T cell activation against Cryptococcus spp. and 18B7 and 2H1 scFv influenced the strength of tonic signaling. 2H1-GXMR-CAR and 18B7-GXMR-CAR are efficiently expressed on the cell surface;2H1-GXMR-CAR and 18B7-GXMR-CAR redirected T cells toward the ligands;18B7-GXMR-CAR provided highest levels of tonic signaling;Binding pocket of 18B7 scFv favored the tonic signaling triggered by GXMR-CAR;Binding pocket of 18B7 scFv favored the tonic signaling triggered by GXMR-CAR; 2H1-GXMR-CAR and 18B7-GXMR-CAR are efficiently expressed on the cell surface; 2H1-GXMR-CAR and 18B7-GXMR-CAR redirected T cells toward the ligands; 18B7-GXMR-CAR provided highest levels of tonic signaling; Binding pocket of 18B7 scFv favored the tonic signaling triggered by GXMR-CAR; Binding pocket of 18B7 scFv favored the tonic signaling triggered by GXMR-CAR;
DOI: 10.6084/m9.figshare.23905711
title: A data-driven machine learning approach for discovering potent LasR inhibitors

description: The rampant spread of multidrug-resistant <i>Pseudomonas aeruginosa</i> strains severely threatens global health. This severity is compounded against the backdrop of a stagnating antibiotics development pipeline. Moreover, with many promising therapeutics falling short of expectations in clinical trials, targeting the <i>las</i> quorum sensing (QS) system remains an attractive therapeutic strategy to combat <i>P. aeruginosa</i> infection. Thus, our primary goal was to develop a drug prediction algorithm using machine learning to identify potent LasR inhibitors. In this work, we demonstrated using a Multilayer Perceptron (MLP) algorithm boosted with AdaBoostM1 to discriminate between active and inactive LasR inhibitors. The optimal model performance was evaluated using 5-fold cross-validation and test sets. Our best model achieved a 90.7% accuracy in distinguishing active from inactive LasR inhibitors, an area under the Receiver Operating Characteristic Curve value of 0.95, and a Matthews correlation coefficient value of 0.81 when evaluated using test sets. Subsequently, we deployed the model against the Enamine database. The top-ranked compounds were further evaluated for their target engagement activity using molecular docking studies, Molecular Dynamics simulations, MM-GBSA analysis, and Free Energy Landscape analysis. Our data indicate that several of our chosen top hits showed better ligand-binding affinities than naringenin, a competitive LasR inhibitor. Among the six top hits, five of these compounds were predicted to be LasR inhibitors that could be used to treat <i>P. aeruginosa</i>-associated infections. To our knowledge, this study provides the first assessment of using an MLP-based QSAR model for discovering potent LasR inhibitors to attenuate <i>P. aeruginosa</i> infections.
DOI: 10.6084/m9.figshare.23905711.v1
title: A data-driven machine learning approach for discovering potent LasR inhibitors

description: The rampant spread of multidrug-resistant <i>Pseudomonas aeruginosa</i> strains severely threatens global health. This severity is compounded against the backdrop of a stagnating antibiotics development pipeline. Moreover, with many promising therapeutics falling short of expectations in clinical trials, targeting the <i>las</i> quorum sensing (QS) system remains an attractive therapeutic strategy to combat <i>P. aeruginosa</i> infection. Thus, our primary goal was to develop a drug prediction algorithm using machine learning to identify potent LasR inhibitors. In this work, we demonstrated using a Multilayer Perceptron (MLP) algorithm boosted with AdaBoostM1 to discriminate between active and inactive LasR inhibitors. The optimal model performance was evaluated using 5-fold cross-validation and test sets. Our best model achieved a 90.7% accuracy in distinguishing active from inactive LasR inhibitors, an area under the Receiver Operating Characteristic Curve value of 0.95, and a Matthews correlation coefficient value of 0.81 when evaluated using test sets. Subsequently, we deployed the model against the Enamine database. The top-ranked compounds were further evaluated for their target engagement activity using molecular docking studies, Molecular Dynamics simulations, MM-GBSA analysis, and Free Energy Landscape analysis. Our data indicate that several of our chosen top hits showed better ligand-binding affinities than naringenin, a competitive LasR inhibitor. Among the six top hits, five of these compounds were predicted to be LasR inhibitors that could be used to treat <i>P. aeruginosa</i>-associated infections. To our knowledge, this study provides the first assessment of using an MLP-based QSAR model for discovering potent LasR inhibitors to attenuate <i>P. aeruginosa</i> infections.
DOI: 10.6084/m9.figshare.24080554
title: Impaired proliferation and migration of HUVEC and melanoma cells by human anti-FGF2 mAbs derived from a murine hybridoma by guided selection

description: Disadvantages of using murine monoclonal antibodies (mAb) in human therapy, such as immunogenicity response, led to the development of technologies to transform murine antibodies into human antibodies. The murine anti-FGF2 3F12E7 mAb was proposed as a promising agent to treat metastatic melanoma tumors; once it blocks the FGF2, responsible for playing a role in tumor growth, angiogenesis, and metastasis. Considering the therapeutic potential of anti-FGF2 3F12E7 mAb and its limited use in humans due to its origin, we used this antibody as the template for a guided selection humanization technique to obtain human anti-FGF2 mAbs. Three Fab libraries (murine, hybrid, and human) were constructed for humanization. The libraries were phage-displayed, and the panning was performed against recombinant human FGF2 (rFGF2). The selected human variable light and heavy chains were cloned into AbVec vectors for full-length IgG expression into HEK293-F cells. Surface plasmon resonance analyses showed binding to rFGF2 of seven mAbs out of 20 expressed. Assays performed with these mAbs resulted in two that showed proliferation reduction and cell migration attenuation of HUVEC and SK-Mel-28 melanoma cells. In-silico analyses predicted that these two human anti-FGF2 mAbs interact with FGF2 at a similar patch of residues than the chimeric anti-FGF2 antibody, comprehending a region within the heparin-binding domains of FGF2, essential for its function. These results are comparable to those achieved by the murine anti-FGF2 3F12E7 mAb and showed success in the humanization process and selection of two human mAbs with the potential to inhibit undesirable FGF2 roles. The guided selection humanization process enabled the production of 20 human mAbs anti-FGF2;Seven human anti-FGF2 mAbs showed binding to the rFGF2 antigen in the SPR binding assay;Two human anti-FGF2 mAbs inhibited the proliferation and migration of HUVEC and SK-Mel-28 cells and were predicted to contact the FGF2 at a similar patch of residues than the original mAb. The guided selection humanization process enabled the production of 20 human mAbs anti-FGF2; Seven human anti-FGF2 mAbs showed binding to the rFGF2 antigen in the SPR binding assay; Two human anti-FGF2 mAbs inhibited the proliferation and migration of HUVEC and SK-Mel-28 cells and were predicted to contact the FGF2 at a similar patch of residues than the original mAb.
DOI: 10.6084/m9.figshare.24080554.v1
title: Impaired proliferation and migration of HUVEC and melanoma cells by human anti-FGF2 mAbs derived from a murine hybridoma by guided selection

description: Disadvantages of using murine monoclonal antibodies (mAb) in human therapy, such as immunogenicity response, led to the development of technologies to transform murine antibodies into human antibodies. The murine anti-FGF2 3F12E7 mAb was proposed as a promising agent to treat metastatic melanoma tumors; once it blocks the FGF2, responsible for playing a role in tumor growth, angiogenesis, and metastasis. Considering the therapeutic potential of anti-FGF2 3F12E7 mAb and its limited use in humans due to its origin, we used this antibody as the template for a guided selection humanization technique to obtain human anti-FGF2 mAbs. Three Fab libraries (murine, hybrid, and human) were constructed for humanization. The libraries were phage-displayed, and the panning was performed against recombinant human FGF2 (rFGF2). The selected human variable light and heavy chains were cloned into AbVec vectors for full-length IgG expression into HEK293-F cells. Surface plasmon resonance analyses showed binding to rFGF2 of seven mAbs out of 20 expressed. Assays performed with these mAbs resulted in two that showed proliferation reduction and cell migration attenuation of HUVEC and SK-Mel-28 melanoma cells. In-silico analyses predicted that these two human anti-FGF2 mAbs interact with FGF2 at a similar patch of residues than the chimeric anti-FGF2 antibody, comprehending a region within the heparin-binding domains of FGF2, essential for its function. These results are comparable to those achieved by the murine anti-FGF2 3F12E7 mAb and showed success in the humanization process and selection of two human mAbs with the potential to inhibit undesirable FGF2 roles. The guided selection humanization process enabled the production of 20 human mAbs anti-FGF2;Seven human anti-FGF2 mAbs showed binding to the rFGF2 antigen in the SPR binding assay;Two human anti-FGF2 mAbs inhibited the proliferation and migration of HUVEC and SK-Mel-28 cells and were predicted to contact the FGF2 at a similar patch of residues than the original mAb. The guided selection humanization process enabled the production of 20 human mAbs anti-FGF2; Seven human anti-FGF2 mAbs showed binding to the rFGF2 antigen in the SPR binding assay; Two human anti-FGF2 mAbs inhibited the proliferation and migration of HUVEC and SK-Mel-28 cells and were predicted to contact the FGF2 at a similar patch of residues than the original mAb.
DOI: 10.6084/m9.figshare.24174580
title: Functional integration of protein A binding ability to antibody fragments for convenient and tag-free purification

description: Although the development of small therapeutic antibodies is important, the affinity tags used for their purification often result in heterogeneous production and immunogenicity. In this study, we integrated <i>Staphylococcus aureus</i> protein A (SpA) binding ability into antibody fragments for convenient and tag-free purification. SpA affinity chromatography is used as a global standard purification method for conventional antibodies owing to its high binding affinity to the Fc region. SpA also has a binding affinity for some variable heavy domains (VH) classified in the VH3 subfamily. Through mutagenesis based on alignment and structural modeling results using the SpA-VH3 cocrystal structure, we integrated the SpA-binding ability into the anti-CD3 single-chain Fv. Furthermore, we applied this mutagenesis approach to more complicated small bispecific antibodies and successfully purified the antibodies using SpA affinity chromatography. The antibodies retained their biological function after purification. Integration of SpA-binding ability into conventional antibody fragments simplifies the purification and monitoring of the production processes and, thus, is an ideal strategy for accelerating the development of small therapeutic antibodies. Furthermore, because of its immunoactivity, the anti-CD3 variable region with SpA-binding ability is an effective building block for developing engineered cancer therapeutic antibodies without the Fc region.