cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/hn4nygwf76.1
title: Calcium dysregulation is the critical initiator in high dose chloroquine-induced programmed cell death of Plasmodium falciparum

description: We investigated an alternative cell death mechanism triggered by micromolar concentrations of the antimalarial chloroquine (CQ) in Plasmodium falciparum. Three “hit” compounds from the Medicines for Malaria Venture (MMV) Pathogen Box were further characterized, leading to the identification of the top-hit compound, MMV085071. Ten analogues of this compound were evaluated using dose-response assays, and one lead analogue, MMV1545561, was selected as the top lead. Transcriptomic changes were analyzed following treatment of parasites with 3 µM of CQ, MMV085071, and MMV1545561 for 4 hours, starting at 32 hours-post-invasion. The raw RNA-seq data from this study is provided below.

A link to the publication will be added upon its release.
DOI: 10.7483/opendata.cms.8fo9.xotp
title: /TprimeBToTH_TLep_Hbb_LH_MT2600_MH450_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.17082971
title: Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia

description: Paired diagnostic and remission samples from 20 adults with core binding factor acute myeloid leukemia (AML), comprising ten with t(8;21)(q22;q22) [RUNX1::RUNX1T1] and ten with inv(16)(p13q22)/t(16;16)(p13;q22) [CBFB::MYH11] analyzed by whole genome sequencing are included in this data set. All patients had de novo AML and the cases were selected based on the availability of good quality DNA from both diagnosis and remission. The median age of the patients was 51.5 years (range 19-74 years) and the female/male ratio was 1:1.5. the Declaration of Helsinki. DNA was extracted from diagnostic and remission bone marrow aspirates and sequencing libraries were constructed using the TruSeq PCR-Free DNA Library Preparation Kit (Illumina, San Diego, CA, USA) followed by cluster generation and 150 cycles paired-end sequencing with the NovaSeq 6000 system and v1.5 sequencing chemistry (Illumina) at the SNP&SEQ Technology Platform, Uppsala University. The data has been used for detection/investigation of single nucleotide variants, mutational signatures, fusion genes and copy number aberrations.<br><br>
DOI: 10.17632/4rwbj9g2k3.1
title: MY DATA

description: This study hypothesizes that a blended learning approach integrating traditional cardiac rehabilitation (CR) with in-person training sessions and remote assistance through an app based on the Knowledge, Attitude, and Practice (KAP) model will improve medication adherence and self-efficacy among patients undergoing coronary artery bypass graft (CABG) surgery compared to traditional CR alone. 
Participants: 70 patients referred to the cardiac rehabilitation program, randomized 1:1 into intervention and control groups (35 patients each). Intervention: Four in-person training sessions and three months of app-based follow-up support, in addition to traditional CR. Assessments: Medication adherence and self-efficacy were measured pre-CR, after 1 month, and 3 months post-CR. 
Baseline: No significant demographic differences between the intervention and control groups. Outcomes: The intervention group showed significant and sustained improvements in medication adherence and self-efficacy compared to the control group (p&lt;0.001). These improvements were observed from the first month and continued throughout the study period.
Enhanced Self-Efficacy: Blended learning may provide patients with more comprehensive education and support, boosting their confidence in managing their health post-surgery. Improved Medication Adherence: Continuous support and follow-up via the app likely contributed to better adherence to medication regimens.
Blended learning in cardiac rehabilitation positively impacts medication adherence and self-efficacy for CABG patients. This approach should be further explored and potentially integrated into standard CR programs to enhance patient outcomes.
DOI: 10.7483/opendata.cms.mdwo.cwoe
title: /TprimeBToTH_TLep_Hbb_LH_MT2600_MH450_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.17082971.v1
title: Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia

description: Paired diagnostic and remission samples from 20 adults with core binding factor acute myeloid leukemia (AML), comprising ten with t(8;21)(q22;q22) [RUNX1::RUNX1T1] and ten with inv(16)(p13q22)/t(16;16)(p13;q22) [CBFB::MYH11] analyzed by whole genome sequencing are included in this data set. All patients had de novo AML and the cases were selected based on the availability of good quality DNA from both diagnosis and remission. The median age of the patients was 51.5 years (range 19-74 years) and the female/male ratio was 1:1.5. the Declaration of Helsinki. DNA was extracted from diagnostic and remission bone marrow aspirates and sequencing libraries were constructed using the TruSeq PCR-Free DNA Library Preparation Kit (Illumina, San Diego, CA, USA) followed by cluster generation and 150 cycles paired-end sequencing with the NovaSeq 6000 system and v1.5 sequencing chemistry (Illumina) at the SNP&SEQ Technology Platform, Uppsala University. The data has been used for detection/investigation of single nucleotide variants, mutational signatures, fusion genes and copy number aberrations.<br><br>
DOI: 10.17632/s4mhj99hcz.1
title: Floral spatial morphological characteristics preferences facilitate mating and predation in flower-visiting spiders

description: Numerous flower visitors exhibit varying preferences for floral characteristics, a topic that has been extensively studied. As one group of flower visitors, the preferences of spiders for flower color have garnered attention; however, their preferences for the spatial morphological characteristics of flowers remain largely unexplored. This study investigated the preferences of flower-visiting crab spiders (Ebrechtella tricuspidata) for flower size, petal density, and symmetry, and explored the underlying reasons from the courtship and predation. The results indicated that male spiders preferred larger flowers, while females favored densely petaled flowers and symmetrical flowers. Additionally, males exhibited a stronger preference for females on larger flowers than on smaller ones. However, no significant differences were observed in males mating selection based on petal density and symmetry. Furthermore, consistent with spider preferences, potential prey, such as houseflies and bees, also showed a significant preference for larger, densely petaled, and symmetrical flowers in visitation experiments. We propose that prey preferences for floral characteristics may be a primary factor influencing spider preferences. We hypothesize that the flower characteristics influence insect visitation preferences, which may extend to third trophic level predators, thereby determining the preferences of flower-visiting spiders.
DOI: 10.17044/scilifelab.17099687
title: Data and code for: Sequence specificity in DNA binding is mainly governed by association

description: Sequence-specific
 binding of proteins to DNA is essential for accessing genetic 
information. Here, we derive
a simple equation for target-site recognition, which uncovers a 
previously unrecognized coupling between the macroscopic association and
 dissociation rates of the searching protein. Importantly, this 
relationship makes it possible to recover the relevant microscopic
rates from experimentally determined macroscopic ones. This post 
contains kinetic data for the lac repressor and code to analyse and 
interpret the data in light of this theory. <br><br>File list:- data_pbm.zip - Data-set for output generated using a protein binding microarray. <br>- data_tirf.zip - Data-set for output generated using TIRF based single molecule localisation microscopy.<br>- data_cas9.zip - Data-set for cas9 binding collected from literature. <br>- data_spr.zip - Data-set for output generated using surface plasmon resonance based methods.<br>- figure_scripts.zip - Set of scripts used to generate all figures. See README file inside for details.
DOI: 10.17044/scilifelab.17099687.v1
title: Data and code for: Sequence specificity in DNA binding is mainly governed by association

description: Sequence-specific
 binding of proteins to DNA is essential for accessing genetic 
information. Here, we derive
a simple equation for target-site recognition, which uncovers a 
previously unrecognized coupling between the macroscopic association and
 dissociation rates of the searching protein. Importantly, this 
relationship makes it possible to recover the relevant microscopic
rates from experimentally determined macroscopic ones. This post 
contains kinetic data for the lac repressor and code to analyse and 
interpret the data in light of this theory. <br><br>File list:- data_pbm.zip - Data-set for output generated using a protein binding microarray. <br>- data_tirf.zip - Data-set for output generated using TIRF based single molecule localisation microscopy.<br>- data_cas9.zip - Data-set for cas9 binding collected from literature. <br>- data_spr.zip - Data-set for output generated using surface plasmon resonance based methods.<br>- figure_scripts.zip - Set of scripts used to generate all figures. See README file inside for details.
DOI: 10.17632/2v3pkvknx2.1
title: An image dataset of hyacinth beans

description: This dataset is on hyacinth bean (also known as-Indian Broad Beans, broad bean) classification, from different regions of Bangladesh. This dataset contains a total of 1978 images and a total of 5 categories based on location. Each location folder contains sub folder.
DOI: 10.7483/opendata.cms.89ki.lf2l
title: /TprimeBToTH_TLep_Hbb_LH_MT2600_MH500_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17632/ppp3677mz7.1
title: Apulia_grapevine_clones

description: VCF Apulia grapevine clones
DOI: 10.15468/dl.4p6388
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hymenalia obscuriceps Pic, 1925",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071194-241126133413365/datasets/export for details.
DOI: 10.7483/opendata.cms.ays0.beuo
title: /TprimeBToTH_TLep_Hbb_LH_MT2600_MH500_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.18020801
title: Data and code related to "Direct measurements of mRNA translation kinetics in living cells", by Metelev et al.

description: This repository contains microscopy data and analysis code related to the publication: Metelev et al., "Direct measurements of mRNA translation kinetics in living cells".<br>The study includes single-particle tracking of ribosomal subunits in live E. coli cells, for analysis of translation kinetics under different conditions.<br>A detailed list of files and file organization can be found in the readme text file.
DOI: 10.17632/hk6d864c9k
title: Instances for "Collect and Process VRP with Completion Time minimization"

description: Instances for "Collect and Process VRP with Completion Time minimization"
DOI: 10.17632/hk6d864c9k.1
title: Instances for "Collect and Process VRP with Completion Time minimization"

description: Instances for "Collect and Process VRP with Completion Time minimization"
DOI: 10.17044/scilifelab.18020801.v1
title: Data and code related to "Direct measurements of mRNA translation kinetics in living cells", by Metelev et al.

description: This repository contains microscopy data and analysis code related to the publication: Metelev et al., "Direct measurements of mRNA translation kinetics in living cells".<br>The study includes single-particle tracking of ribosomal subunits in live E. coli cells, for analysis of translation kinetics under different conditions.<br>A detailed list of files and file organization can be found in readme.pdf.
DOI: 10.7483/opendata.cms.r839.gszp
title: /TprimeBToTH_TLep_Hbb_LH_MT2600_MH50_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17632/93cxyyb7gx.1
title: Preoperative anxiety in ophthalmic surgery

description: A total of 339 patients who underwent vision correction surgery completed a Spielberger anxiety questionnaire to assess their preoperative anxiety levels, as well as a research questionnaire that included questions about their gender, age, medical history (including previous surgical interventions and any concomitant medical conditions), the duration of surgery, the use of intravenous anesthesia (specifically Elsepam 1 mg and Fentanyl 50 mcg), and the occurrence of any adverse events such as hypotension, postoperative nausea, and vomiting.
DOI: 10.7483/opendata.cms.uv7k.e5hj
title: /TprimeBToTH_TLep_Hbb_LH_MT2600_MH50_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.7483/opendata.cms.mbx7.2cii
title: /TprimeBToTH_TLep_Hbb_LH_MT2600_MH75_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16MiniAODv2-106X_mcRun2_asymptotic_v17-v2/MINIAODSIM
DOI: 10.17044/scilifelab.19154459
title: Hyperthermia-induced in situ drug amorphization by superparamagnetic nanoparticles in oral dosage forms

description: Superparamagnetic iron oxide nanoparticles (SPIONs)
generate heat upon exposure to an alternating magnetic field (AMF) which has
been studied for hyperthermia treatment and triggered drug release. This study
introduces a novel application of magnetic hyperthermia to induce amorphization
of a poorly aqueous soluble drug, celecoxib, in situ in tablets for oral administration. In situ
amorphization can overcome the drug development hurdle of poor aqueous
solubility by molecularly dispersing the drug in a polymeric network inside a
tablet. However, current shortcomings of this approach include low drug loading
in the tablets, toxicity of enabling excipients, and drug degradation. Here,
SPIONs produced by flame spray pyrolysis are compacted with polyvinylpyrolidone
and celecoxib, and exposed to an AMF. The degree of amorphization is strongly
linked to the maximum tablet temperature achieved during AMF exposure, which
depends on SPION composition and content in the tablets. Manganese ferrites
exhibit no toxicity in human intestinal Caco-2 cell lines and are more
effective than zinc ferrites in inducing complete amorphization of celecoxib.
The resulting rapid dissolution and high solubility of in situ amorphized celecoxib in biorelevant intestinal fluid
demonstrates the promising capability of SPIONs as enabling excipients to
magnetically induce amorphization<i> </i>in
situ in oral dosage forms.
DOI: 10.17044/scilifelab.19154459.v1
title: Hyperthermia-induced in situ drug amorphization by superparamagnetic nanoparticles in oral dosage forms

description: Superparamagnetic iron oxide nanoparticles (SPIONs)
generate heat upon exposure to an alternating magnetic field (AMF) which has
been studied for hyperthermia treatment and triggered drug release. This study
introduces a novel application of magnetic hyperthermia to induce amorphization
of a poorly aqueous soluble drug, celecoxib, in situ in tablets for oral administration. In situ
amorphization can overcome the drug development hurdle of poor aqueous
solubility by molecularly dispersing the drug in a polymeric network inside a
tablet. However, current shortcomings of this approach include low drug loading
in the tablets, toxicity of enabling excipients, and drug degradation. Here,
SPIONs produced by flame spray pyrolysis are compacted with polyvinylpyrolidone
and celecoxib, and exposed to an AMF. The degree of amorphization is strongly
linked to the maximum tablet temperature achieved during AMF exposure, which
depends on SPION composition and content in the tablets. Manganese ferrites
exhibit no toxicity in human intestinal Caco-2 cell lines and are more
effective than zinc ferrites in inducing complete amorphization of celecoxib.
The resulting rapid dissolution and high solubility of in situ amorphized celecoxib in biorelevant intestinal fluid
demonstrates the promising capability of SPIONs as enabling excipients to
magnetically induce amorphization<i> </i>in
situ in oral dosage forms.
DOI: 10.17632/z4xwhkjy8m.1
title: Natural resources rent, financial sector development, institutional quality and environmental degradation

description: Data on the impact of natural resources rent, institutional quality and financial sector development on the environment. The data includes control variables of trade, FDI and renewable energy consumption.
DOI: 10.17044/scilifelab.19160954
title: Single cell whole genome sequencing of high hyperdiploid acute lymphoblastic leukemia

description:   
This dataset included 577 samples with high hyperdiploid acute lymphoblastic leukemia (ALL) that were collected from four different cohorts: the Division of Clinical Genetics, Lund University, Sweden, Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic (Zaliova et al., 2016), Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France (Duployez et al., 2018), and The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) program (NCBI dbGAP accession number phs00464). All samples were genotyped using either the Affymetrix SNP Array, Illumina's BeadArray platform or the whole genome/exome sequencing by the Illumina platform.  Nine high hyperdiploid ALL samples and one normal bone marrow sample were subjected to low pass single cell whole genome sequencing with the median sequencing coverage of 0.02x. Single nuclei in G0/G1 phase were isolated using a fluorescence-activated cell sorting (FACS) cytometer. DNA libraries were constructed and associated next-generation sequencing was carried out by European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. Further details regarding the DNA libraries construction are available by Bos et. al., 2019 (https://link.springer.com/protocol/10.1007/978-1-4939-8931-7_15). The dataset has been used for copy number aberrations analysis. The raw data file can be made available after applying for access and agreeing to the terms and conditions for use.
DOI: 10.7483/opendata.cms.0vwv.nfvh
title: /TprimeBToTH_TLep_Hbb_LH_MT2600_MH75_TuneCP5_13TeV-madgraph-pythia8/RunIISummer20UL16NanoAODv9-106X_mcRun2_asymptotic_v17-v1/NANOAODSIM
DOI: 10.17044/scilifelab.19248172
title: Test dataset from: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

description: This item contains a test dataset based on Sumatran rhinoceros (<em>Dicerorhinus sumatrensis</em>) whole-genome re-sequencing data that we publish along with the GenErode pipeline (https://github.com/NBISweden/GenErode; Kutschera et al. 2022) and that we reduced in size so that users have the possibility to get familiar with the pipeline before analyzing their own genome-wide datasets.
We extracted scaffold ‘Sc9M7eS_2_HRSCAF_41’ of size 40,842,778 bp from the Sumatran rhinoceros genome assembly (<em>Dicerorhinus sumatrensis harrissoni</em>; GenBank accession number GCA_014189135.1) to be used as reference genome in GenErode. Some GenErode steps require the reference genome of a closely related species, so we additionally provide three scaffolds from the White rhinoceros genome assembly (<em>Ceratotherium simum simum</em>; GenBank accession number GCF_000283155.1) with a combined length of 41,195,616 bp that are putatively orthologous to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with gene predictions in GTF format. The repository also contains a Sumatran rhinoceros mitochondrial genome (GenBank accession number NC_012684.1) to be used as reference for the optional mitochondrial mapping step in GenErode.
The test dataset contains whole-genome re-sequencing data from three historical and three modern Sumatran rhinoceros samples from the now-extinct Malay Peninsula population from von Seth et al. (2021) that was subsampled to paired-end reads that mapped to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with a small proportion of randomly selected reads that mapped to the Sumatran rhinoceros mitochondrial genome or elsewhere in the genome.
For GERP analyses, scaffolds from the genome assemblies of 30 mammalian outgroup species are provided that had reciprocal blast hits to gene predictions from Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’. Further, a phylogeny of the White rhinoceros and the 30 outgroup species including divergence time estimates (in billions of years) from timetree.org is available.
Finally, the item contains configuration and metadata files that were used for three separate runs of GenErode to generate the results presented in Kutschera et al. (2022).
Bash scripts and a workflow description for the test dataset generation are available in the GenErode GitHub repository (https://github.com/NBISweden/GenErode/docs/extras/test_dataset_generation).
<br>
References:
Kutschera VE, Kierczak M, van der Valk T, von Seth J, Dussex N, Lord E, et al. GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. BMC Bioinformatics 2022;23:228. https://doi.org/10.1186/s12859-022-04757-0
von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, et al. Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations. Nature Communications 2021;12:2393.