cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12873023
title: Additional file 3 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 3:PCR and oligonucleotide probes used in the Sequenom MassARRAY platform for SNP typing. List of SNP loci genotyped using the Sequenom MassARRAY platform. The PCR primers, the oligonuocletide probes and the multiplex information are shown. The sequences of the SNP flanking regions have been deposited in NCBI dbSNP. (XLS 46 KB)
DOI: 10.6084/m9.figshare.12873044.v9
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
DOI: 10.6084/m9.figshare.12873023.v1
title: Additional file 3 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 3:PCR and oligonucleotide probes used in the Sequenom MassARRAY platform for SNP typing. List of SNP loci genotyped using the Sequenom MassARRAY platform. The PCR primers, the oligonuocletide probes and the multiplex information are shown. The sequences of the SNP flanking regions have been deposited in NCBI dbSNP. (XLS 46 KB)
DOI: 10.6084/m9.figshare.12873029
title: Additional file 5 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 5:Blast hits results based on the NCBI non-redundant protein database. List of species whose sequences showed significant homology to the EST sequences from Daphnia magna, based on similarities by BLAST searches in the NCBI non-redundant protein database. For each species the number of hits found is listed in the second column of the table. In total, 651 of the 685 EST sequences showed homology to sequences in other species. The list of different genes identified in the dataset ('genes'), the redundancy of the identified genes ('genes redundancy') and the number of times in which each gene was found in different species ('redundancy in species') are also shown. (XLS 50 KB)
DOI: 10.6084/m9.figshare.12873032
title: Additional file 6 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 6:List of the EST-linked SNP and descriptive statistics. List of SNP markers in the set of 147 SNP targeted for genotyping with the Sequenom MassARRAY platform. The protein changes both at the synonymous (S) and the non-synonymous (NS) sites, the codon position of the point mutation, the genotyping success rate, and the minor allele frequency are shown. The characteristics of the contigs from where the SNPs were developed are also shown, in terms of length, polymorphism, and number of sequences in the contig. Nr: SNPs that did not fit in any assay design. (XLS 56 KB)
DOI: 10.6084/m9.figshare.12873035
title: Additional file 7 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 7:Features of the EST contigs from which SNP markers were developed. Main features of the EST contigs from which SNP markers were designed. The contigs of the SNPs that failed in the genotyping process and the ones with a success rate larger than 70% are shown. (XLS 18 KB)
DOI: 10.6084/m9.figshare.12873038.v1
title: Additional file 8 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 8:Population genetic statistics in the six natural populations used for the SNPs validation. Population genetic statistics in the set of six populations used to validate the SNP markers. Ho = observed heterozigosity; He = expected heterozigosity, frequency of the two SNP alleles in the population, H-W = Hardy-Weinberg disequilibrium test (P &lt; 0.05). (XLS 60 KB)
DOI: 10.6084/m9.figshare.12873032.v1
title: Additional file 6 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 6:List of the EST-linked SNP and descriptive statistics. List of SNP markers in the set of 147 SNP targeted for genotyping with the Sequenom MassARRAY platform. The protein changes both at the synonymous (S) and the non-synonymous (NS) sites, the codon position of the point mutation, the genotyping success rate, and the minor allele frequency are shown. The characteristics of the contigs from where the SNPs were developed are also shown, in terms of length, polymorphism, and number of sequences in the contig. Nr: SNPs that did not fit in any assay design. (XLS 56 KB)
DOI: 10.6084/m9.figshare.12873041
title: Additional file 9 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 9:Gene function of the contigs where SNP outliers were detected. List of outlier loci and the corresponding EST sequences with accession numbers to NCBI GenBank from which the SNPs were developed. The gene function was inferred from the EST contigs. (XLS 37 KB)
DOI: 10.6084/m9.figshare.12873044
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
DOI: 10.6084/m9.figshare.12873044.v11
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
DOI: 10.6084/m9.figshare.12873044.v13
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
DOI: 10.6084/m9.figshare.12873020
title: Additional file 2 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 2:Natural populations of Daphnia magna used for SNP validation and their environmental characteristics. List of populations from Belgium used for SNP validation and their environmental characteristics. N = population size; Fish = presence (1)/absence (0) of fish; Land use = high (1)/low (0) land use intensity; Parasite = presence (1)/absence (0) of the parasite Pasteuria ramosa. Sampling date and environmental variables as measured at the sampling sites are also listed. Transparency was measured by means of Secchi disk. (XLS 20 KB)
DOI: 10.6084/m9.figshare.12873041.v1
title: Additional file 9 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 9:Gene function of the contigs where SNP outliers were detected. List of outlier loci and the corresponding EST sequences with accession numbers to NCBI GenBank from which the SNPs were developed. The gene function was inferred from the EST contigs. (XLS 37 KB)
DOI: 10.6084/m9.figshare.12873038
title: Additional file 8 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 8:Population genetic statistics in the six natural populations used for the SNPs validation. Population genetic statistics in the set of six populations used to validate the SNP markers. Ho = observed heterozigosity; He = expected heterozigosity, frequency of the two SNP alleles in the population, H-W = Hardy-Weinberg disequilibrium test (P &lt; 0.05). (XLS 60 KB)
DOI: 10.6084/m9.figshare.12873044.v10
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
DOI: 10.6084/m9.figshare.7991933
title: AdditionalFile5.csv

description: Table S4Maximum symptom score of 71 previously uncharacterized <i>M. truncatula</i> accessions in response to root infection by <i>V. alfalfae</i>. Expected phenotype, based on their geographical proximity with resistant or susceptible reference accessions <br>
DOI: 10.6084/m9.figshare.12873044.v12
title: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
DOI: 10.6084/m9.figshare.12873029.v1
title: Additional file 5 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 5:Blast hits results based on the NCBI non-redundant protein database. List of species whose sequences showed significant homology to the EST sequences from Daphnia magna, based on similarities by BLAST searches in the NCBI non-redundant protein database. For each species the number of hits found is listed in the second column of the table. In total, 651 of the 685 EST sequences showed homology to sequences in other species. The list of different genes identified in the dataset ('genes'), the redundancy of the identified genes ('genes redundancy') and the number of times in which each gene was found in different species ('redundancy in species') are also shown. (XLS 50 KB)
DOI: 10.6084/m9.figshare.7991933.v1
title: AdditionalFile5.csv

description: Table S4Maximum symptom score of 71 previously uncharacterized <i>M. truncatula</i> accessions in response to root infection by <i>V. alfalfae</i>. Expected phenotype, based on their geographical proximity with resistant or susceptible reference accessions <br>
DOI: 10.6084/m9.figshare.12873035.v1
title: Additional file 7 of Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

description: Additional file 7:Features of the EST contigs from which SNP markers were developed. Main features of the EST contigs from which SNP markers were designed. The contigs of the SNPs that failed in the genotyping process and the ones with a success rate larger than 70% are shown. (XLS 18 KB)
DOI: 10.6084/m9.figshare.7991930
title: AdditionalFile4.csv

description: Table S3 Maximum symptom score of 262 <i>M. truncatula</i> accessions in response to root infection by <i>V. alfalfae</i>.
DOI: 10.6084/m9.figshare.7991924
title: Blood proteome profiling using aptamer-based technology for rejection biomarker discovery in transplantation

description: In this study, blood proteome characterization in face transplantation using longitudinal serum samples from six face transplant patients was carried out with SOMAscan platform. Overall, 24 serum samples from 13 no-rejection, 5 nonsevere rejection and 6 severe rejection episodes were analyzed.<br>Files attached:<br><b><i>HMS-16-007.20160218.adat </i></b>- raw SomaScan dataset presented in adat format.<b><i></i></b><br><b><i>HMS-16-007_SQS_20160218.pdf </i></b>- technical validation report on the dataset.<br><b><i>HMS-16-007.HybNorm.20160218.adat </i></b>- SomaScan dataset after hybridization control normalization presented in <i>adat </i>format.<b><i></i></b><br><b><i>HMS-16-007.HybNorm.MedNorm.20160218.adat </i></b>- SomaScan dataset after hybridization control normalization and median signal normalization presented in <i>adat </i>format.<b><i><br></i></b><b><i>HMS-16-007.HybNorm.MedNorm.Cal.20160218.adat </i></b>- SomaScan dataset after hybridization control normalization, median signal normalization, and calibration presented in <i>adat </i>format.<br><b><i>HMS-16-007.HybNorm.MedNorm.Cal.20160218.xls </i></b><i>- </i>SomaScan dataset after hybridization control normalization, median signal normalization, and calibration presented in Microsoft Excel Spreadsheet format.<b><br></b><b><i>Patients_metadata.txt</i> </b>– metadata file containing patients’ demographic and clinical information presented in tab-delimited text format. Metadata is linked to records in the SomaScan dataset via ‘SampleType’ column.<b></b><b><i><br></i></b><b><i>SciData_R_script.R </i></b>– this script is given as an example of a downstream statistical analysis of the HMS-16-007.HybNorm.MedNorm.Cal.20160218.adat dataset.<br><br><b><i>SciData_R_script_SessionInfo</i></b> - Session information for SciData_R_script.R script.<br><br><br>
DOI: 10.6084/m9.figshare.7991927
title: American Geophysical Union Annual Meeting Tweets 2018

description: Archive of ~134k tweets posted between November 25, 2018 and January 1, 2019 with the hashtag #AGU18 OR #AGU2018. Retrieved using TAGS v6.1.7 (http://tags.hawksey.info)
DOI: 10.6084/m9.figshare.7991930.v1
title: AdditionalFile4.csv

description: Table S3 Maximum symptom score of 262 <i>M. truncatula</i> accessions in response to root infection by <i>V. alfalfae</i>.
DOI: 10.6084/m9.figshare.7991903
title: INTRAOPERATIVE BLOOD SALVAGE TECHNIQUE

description: <b>BACKGROUND:</b> Intra-peritoneal blood salvage following massive blood loss in surgical settings is relatively uncommon and a matter of interest for clinicians in general. There have been, however, few reports of such cases in the literature. Any blood salvage procedure perhaps may be a life-saving measure, especially in scenario where compatible homologous blood is not readily available. The rarity of occurrence and clinical curiosity of this entity suggest reporting of this unusual clinical event. <b>CASE PRESENTATION:</b> We report the intra-operative blood collection and subsequent re-transfusion in a 22-year-old Cameroonian primigravida lady. She was hemodynamically unstable following massive intra-peritoneal hemorrhage from a ruptured ectopic gestation. Incidentally, this index patient was successfully resuscitated with timely and appropriate resuscitative measures. She went ahead to have emergency open pelvic exploration and right salpingectomy with good post-operative outcome and recovery. <b>CONCLUSIONS:</b> The practice of intra-operative blood salvage techniques as an antidote to massive blood loss is far from being the reality in most clinical settings. With respect to cost savings associated with the use of intra-operative blood salvage, this becomes relatively significant only when there is a high blood loss and a high blood salvage rate. This case report elaborates the benefits inherent in simple intra-operative blood salvage program with an improvised Johnson’s blood salvage kits used in the index patient; that proved practicable, cost-effective to implement in a busy surgical unit and especially those within resource constrained settings.
DOI: 10.6084/m9.figshare.7991927.v1
title: American Geophysical Union Annual Meeting Tweets 2018

description: Archive of ~134k tweets posted between November 25, 2018 and January 1, 2019 with the hashtag #AGU18 OR #AGU2018. Retrieved using TAGS v6.1.7 (http://tags.hawksey.info)
DOI: 10.6084/m9.figshare.7991888
title: The rs17084733 variant in the <i>KIT</i> 3’ UTR disrupts a miR-221/222 binding site in gastrointestinal stromal tumour: a sponge-like mechanism conferring disease susceptibility

description: Several miRNAs are dysregulated in gastrointestinal stromal tumours (GIST), and miR-221/222 appear to have a prominent role in GIST biology. Therefore, we investigated the role of DNA variants located in miR-221/222 precursor sequences and their target <i>KIT</i> 3'UTR. Ninety-five polymorphisms were analysed in 115 GIST cases and 88 healthy controls. <i>KIT</i> 3'UTR rs17084733 and pri-miR-222 rs75246947 were found significantly associated with GIST susceptibility. Specifically, <i>KIT</i> rs17084733 A allele was more common in GIST, particularly in KIT wild-type (WT) patients (Padj = 0.017). rs17084733 variant is located within one of the three miR-221/222 binding sites in the <i>KIT</i> 3'UTR, resulting in a mismatch in this seed region. Conversely, KIT mRNA levels were lower in patients carrying the variant allele, except for <i>KIT</i> mutant GIST. Luciferase assay data in GIST cells, generated using a construct containing all the three miR-221/222 binding sites, are consistent with KIT mRNA levels in GIST patients. Reporter assay data, generated using a construct containing only the site encompassing rs17084733, confirmed that this is a functional variant disrupting the miR-221/222 binding site. In conclusion, this is the first study investigating the role of SNPs on miR-221/222 precursor sequences and their binding region on <i>KIT</i> 3'UTR in GIST. We identified the <i>KIT</i> variant rs17084733 as a possible novel genetic biomarker for risk of developing <i>KIT</i>-WT GIST. Moreover, our findings suggest the role of one of the three miR-221/222 binding sites on <i>KIT</i> 3'UTR as endogenous sponge, soaking up and subtracting miR-221/222 to the other two sites characterized by a higher affinity.
DOI: 10.6084/m9.figshare.7991876
title: Distinctions among electroconvulsion- and proconvulsant-induced seizure discharges and native motor patterns during flight and grooming: quantitative spike pattern analysis in <i>Drosophila</i> flight muscles

description: In <i>Drosophila</i>, high-frequency electrical stimulation across the brain triggers a highly stereotypic repertoire of spasms. These electroconvulsive seizures (ECS) manifest as distinctive spiking discharges across the nervous system and can be stably assessed throughout the seizure repertoire in the large indirect flight muscles dorsal longitudinal muscles (DLMs) to characterize modifications in seizure-prone mutants. However, the relationships between ECS-spike patterns and native motor programs, including flight and grooming, are not known and their similarities and distinctions remain to be characterized. We employed quantitative spike pattern analyses for the three motor patterns including: (1) overall firing frequency, (2) spike timing between contralateral fibers, and (3) short-term variability in spike interval regularity (CV<sub>2</sub>) and instantaneous firing frequency (ISI<sup>−1</sup>). This base-line information from wild-type (WT) flies facilitated quantitative characterization of mutational effects of major neurotransmitter systems: excitatory cholinergic (<i>Cha</i>), inhibitory GABAergic (<i>Rdl</i>) and electrical (<i>ShakB</i>) synaptic transmission. The results provide an initial glimpse on the vulnerability of individual motor patterns to different perturbations. We found marked alterations of ECS discharge spike patterns in terms of either seizure threshold, spike frequency or spiking regularity. In contrast, no gross alterations during grooming and a small but noticeable reduction of firing frequency during <i>Rdl</i> mutant flight were found, suggesting a role for GABAergic modulation of flight motor programs. Picrotoxin (PTX), a known pro-convulsant that inhibits GABA<sub>A</sub> receptors, induced DLM spike patterns that displayed some features, e.g. left-right coordination and ISI<sup>−1</sup> range, that could be found in flight or grooming, but distinct from ECS discharges. These quantitative techniques may be employed to reveal overlooked relationships among aberrant motor patterns as well as their links to native motor programs.
DOI: 10.6084/m9.figshare.7991888.v2
title: The rs17084733 variant in the <i>KIT</i> 3’ UTR disrupts a miR-221/222 binding site in gastrointestinal stromal tumour: a sponge-like mechanism conferring disease susceptibility

description: Several miRNAs are dysregulated in gastrointestinal stromal tumours (GIST), and miR-221/222 appear to have a prominent role in GIST biology. Therefore, we investigated the role of DNA variants located in miR-221/222 precursor sequences and their target <i>KIT</i> 3'UTR. Ninety-five polymorphisms were analysed in 115 GIST cases and 88 healthy controls. <i>KIT</i> 3'UTR rs17084733 and pri-miR-222 rs75246947 were found significantly associated with GIST susceptibility. Specifically, <i>KIT</i> rs17084733 A allele was more common in GIST, particularly in KIT wild-type (WT) patients (Padj = 0.017). rs17084733 variant is located within one of the three miR-221/222 binding sites in the <i>KIT</i> 3'UTR, resulting in a mismatch in this seed region. Conversely, KIT mRNA levels were lower in patients carrying the variant allele, except for <i>KIT</i> mutant GIST. Luciferase assay data in GIST cells, generated using a construct containing all the three miR-221/222 binding sites, are consistent with KIT mRNA levels in GIST patients. Reporter assay data, generated using a construct containing only the site encompassing rs17084733, confirmed that this is a functional variant disrupting the miR-221/222 binding site. In conclusion, this is the first study investigating the role of SNPs on miR-221/222 precursor sequences and their binding region on <i>KIT</i> 3'UTR in GIST. We identified the <i>KIT</i> variant rs17084733 as a possible novel genetic biomarker for risk of developing <i>KIT</i>-WT GIST. Moreover, our findings suggest the role of one of the three miR-221/222 binding sites on <i>KIT</i> 3'UTR as endogenous sponge, soaking up and subtracting miR-221/222 to the other two sites characterized by a higher affinity.
DOI: 10.6084/m9.figshare.7991876.v1
title: Distinctions among electroconvulsion- and proconvulsant-induced seizure discharges and native motor patterns during flight and grooming: quantitative spike pattern analysis in <i>Drosophila</i> flight muscles

description: In <i>Drosophila</i>, high-frequency electrical stimulation across the brain triggers a highly stereotypic repertoire of spasms. These electroconvulsive seizures (ECS) manifest as distinctive spiking discharges across the nervous system and can be stably assessed throughout the seizure repertoire in the large indirect flight muscles dorsal longitudinal muscles (DLMs) to characterize modifications in seizure-prone mutants. However, the relationships between ECS-spike patterns and native motor programs, including flight and grooming, are not known and their similarities and distinctions remain to be characterized. We employed quantitative spike pattern analyses for the three motor patterns including: (1) overall firing frequency, (2) spike timing between contralateral fibers, and (3) short-term variability in spike interval regularity (CV<sub>2</sub>) and instantaneous firing frequency (ISI<sup>−1</sup>). This base-line information from wild-type (WT) flies facilitated quantitative characterization of mutational effects of major neurotransmitter systems: excitatory cholinergic (<i>Cha</i>), inhibitory GABAergic (<i>Rdl</i>) and electrical (<i>ShakB</i>) synaptic transmission. The results provide an initial glimpse on the vulnerability of individual motor patterns to different perturbations. We found marked alterations of ECS discharge spike patterns in terms of either seizure threshold, spike frequency or spiking regularity. In contrast, no gross alterations during grooming and a small but noticeable reduction of firing frequency during <i>Rdl</i> mutant flight were found, suggesting a role for GABAergic modulation of flight motor programs. Picrotoxin (PTX), a known pro-convulsant that inhibits GABA<sub>A</sub> receptors, induced DLM spike patterns that displayed some features, e.g. left-right coordination and ISI<sup>−1</sup> range, that could be found in flight or grooming, but distinct from ECS discharges. These quantitative techniques may be employed to reveal overlooked relationships among aberrant motor patterns as well as their links to native motor programs.
DOI: 10.6084/m9.figshare.12873122.v2
title: Additional file of MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

description: Additional file of MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters