cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4224299
title: Supplementary Material for: Hearing Restoration for Adults with Vestibular Schwannoma in the Only Hearing Ear: Ipsilateral or Contralateral Cochlear Implantation?

description: <i>Objective:</i> To explore auditory outcomes following cochlear implantation (CI) in patients with vestibular schwannoma (VS) in the only hearing ear. <i>Methods:</i> Three patients, all with a long history of hearing loss on one side and with newly diagnosed VS on the other side, underwent ipsilateral or contralateral CI. Their clinical data were collected retrospectively. Postoperative hearing outcomes were measured during follow-up and compared with the preoperative test results. A thorough search of the English-language literature was performed. <i>Results:</i> Patients 1 and 2 underwent CI in the ipsilateral and contralateral ear, respectively, without tumor removal; patient 3 underwent CI after tumor resection. At the last follow-up, the result of pure-tone audiometry was 25, 45, and 25 dB, respectively. An open-set speech discrimination score was achieved in all 3 patients, with monosyllabic word recognition of 60, 30, and 75%, respectively. Besides the patients included in our study, 28 CI cases with VS in the only hearing ear have been reported up to now. <i>Conclusions:</i> In patients with VS in the only hearing ear, significant hearing deterioration with no obvious tumor growth is a good indication for ipsilateral CI. Long-term deafness in the tumor-free ear is not an absolute contraindication for CI.
DOI: 10.6084/m9.figshare.4224299.v1
title: Supplementary Material for: Hearing Restoration for Adults with Vestibular Schwannoma in the Only Hearing Ear: Ipsilateral or Contralateral Cochlear Implantation?

description: <i>Objective:</i> To explore auditory outcomes following cochlear implantation (CI) in patients with vestibular schwannoma (VS) in the only hearing ear. <i>Methods:</i> Three patients, all with a long history of hearing loss on one side and with newly diagnosed VS on the other side, underwent ipsilateral or contralateral CI. Their clinical data were collected retrospectively. Postoperative hearing outcomes were measured during follow-up and compared with the preoperative test results. A thorough search of the English-language literature was performed. <i>Results:</i> Patients 1 and 2 underwent CI in the ipsilateral and contralateral ear, respectively, without tumor removal; patient 3 underwent CI after tumor resection. At the last follow-up, the result of pure-tone audiometry was 25, 45, and 25 dB, respectively. An open-set speech discrimination score was achieved in all 3 patients, with monosyllabic word recognition of 60, 30, and 75%, respectively. Besides the patients included in our study, 28 CI cases with VS in the only hearing ear have been reported up to now. <i>Conclusions:</i> In patients with VS in the only hearing ear, significant hearing deterioration with no obvious tumor growth is a good indication for ipsilateral CI. Long-term deafness in the tumor-free ear is not an absolute contraindication for CI.
DOI: 10.6084/m9.figshare.4224258
title: ESD-Fold.zip

description: File index.php is the first file that the server loads from the folder ESD-Fold. The executable file of the ESD-Fold program is available in Site.exe, and its source code is in file ESD-FOLD-Source.zip.File RNAsequences.zip includes 2 datasets called 15RNAsWithSHAPE and RNA_STRAND_data used in our program. 15RNAsWithSHAPE contains 15 RNA sequences with their available SHAPE data, while RNA_STRAND_data contains 8 families of RNA-Strand dataset, in which SHAPE data is not available.
DOI: 10.6084/m9.figshare.4224246
title: Ligand-based and e-pharmacophore modeling, 3D-QSAR and hierarchical virtual screening to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3)

description: The clinical efficacy of multiple kinase inhibitors has caught the interest of Pharmaceutical and Biotech researchers to develop potential drugs with multi-kinase inhibitory activity for complex diseases. In the present work, we attempted to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3), keys players in immune signaling, by developing ideal pharmacophores integrating Ligand-based pharmacophore models (LBPMs) and Structure-based pharmacophore models (SBPMs), thereby projecting the optimum pharmacophoric required for inhibition of both the kinases. The four point LBPM; ADPR.14 suggested the presence of one hydrogen bond acceptor, one hydrogen bond donor, one positive ionizable, and one ring aromatic feature for Syk inhibitory activity and AADH.54 proposed the necessity of two hydrogen bond acceptor, one hydrogen bond donor, and one hydrophobic feature for JAK3 inhibitory activity. To our interest, SBPMs identified additional ring aromatic features required for inhibition of both the kinases. For Syk inhibitory activity, the hydrogen bond acceptor feature indicated by LBPM was devoid of forming hydrogen bonding interaction with the hinge region amino acid residue (Ala451). Thus merging the information revealed by both LBPMs and SBPMs, ideal pharmacophore models i.e. ADPRR.14 (Syk) and AADHR.54 (JAK3) were generated. These models after rigorous statistical validation were used for screening of Asinex database. The systematic virtual screening protocol, including pharmacophore and docking-based screening, ADME property, and MM-GBSA energy calculations, retrieved final 10 hits as dual inhibitors of Syk and JAK3. Final 10 hits thus obtained can aid in the development of potential therapeutic agents for autoimmune disorders. Also the top two hits were evaluated against both the enzymes.
DOI: 10.6084/m9.figshare.4224246.v1
title: Ligand-based and e-pharmacophore modeling, 3D-QSAR and hierarchical virtual screening to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3)

description: The clinical efficacy of multiple kinase inhibitors has caught the interest of Pharmaceutical and Biotech researchers to develop potential drugs with multi-kinase inhibitory activity for complex diseases. In the present work, we attempted to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3), keys players in immune signaling, by developing ideal pharmacophores integrating Ligand-based pharmacophore models (LBPMs) and Structure-based pharmacophore models (SBPMs), thereby projecting the optimum pharmacophoric required for inhibition of both the kinases. The four point LBPM; ADPR.14 suggested the presence of one hydrogen bond acceptor, one hydrogen bond donor, one positive ionizable, and one ring aromatic feature for Syk inhibitory activity and AADH.54 proposed the necessity of two hydrogen bond acceptor, one hydrogen bond donor, and one hydrophobic feature for JAK3 inhibitory activity. To our interest, SBPMs identified additional ring aromatic features required for inhibition of both the kinases. For Syk inhibitory activity, the hydrogen bond acceptor feature indicated by LBPM was devoid of forming hydrogen bonding interaction with the hinge region amino acid residue (Ala451). Thus merging the information revealed by both LBPMs and SBPMs, ideal pharmacophore models i.e. ADPRR.14 (Syk) and AADHR.54 (JAK3) were generated. These models after rigorous statistical validation were used for screening of Asinex database. The systematic virtual screening protocol, including pharmacophore and docking-based screening, ADME property, and MM-GBSA energy calculations, retrieved final 10 hits as dual inhibitors of Syk and JAK3. Final 10 hits thus obtained can aid in the development of potential therapeutic agents for autoimmune disorders. Also the top two hits were evaluated against both the enzymes.
DOI: 10.6084/m9.figshare.4224243
title: Waiving chronic fish tests: possible use of acute-to-chronic relationships and interspecies correlations

description: EU chemicals legislation requires the use of all available information for hazard and risk assessment before new tests on vertebrates are proposed or conducted. In this context, extrapolation approaches for avoiding chronic fish testing on the basis of existing data have been explored. Simple linear relationships and interspecies sensitivity ratios between <i>Daphnia</i> and fish were calculated and acute-to-chronic relationships and ratios were calculated for fish, taking into consideration the mode of action. The best fitted relationships for the prediction of chronic fish toxicity are obtained based on acute fish and <i>Daphnia</i> data. Chemicals acting by unspecific reactivity and non-polar narcosis give the strongest acute and chronic <i>Daphnia</i>-to-chronic fish relationship. With acute fish data, strong relationships are obtained for all mode of action. <i>Daphnia</i> was found to be more sensitive than fish to several aniline derivatives and pesticides acting through cholinesterase inhibition, and less sensitive than fish to known endocrine disruptors. Extreme (i.e. &lt;1 or &gt;100) interspecies sensitivity ratios were mainly evident for chemicals acting by polar narcosis and specific reactivity. The safety factor of 100 commonly applied in environmental risk assessment does not seem to be equally protective for each mode of action.
DOI: 10.6084/m9.figshare.4224228
title: Mass density measurement of mineralized tissue with grating-based x-ray phase tomography

description: raw synchrotron data of a grating-based X-ray phase tomography of teeth <br>
DOI: 10.6084/m9.figshare.4224243.v1
title: Waiving chronic fish tests: possible use of acute-to-chronic relationships and interspecies correlations

description: EU chemicals legislation requires the use of all available information for hazard and risk assessment before new tests on vertebrates are proposed or conducted. In this context, extrapolation approaches for avoiding chronic fish testing on the basis of existing data have been explored. Simple linear relationships and interspecies sensitivity ratios between <i>Daphnia</i> and fish were calculated and acute-to-chronic relationships and ratios were calculated for fish, taking into consideration the mode of action. The best fitted relationships for the prediction of chronic fish toxicity are obtained based on acute fish and <i>Daphnia</i> data. Chemicals acting by unspecific reactivity and non-polar narcosis give the strongest acute and chronic <i>Daphnia</i>-to-chronic fish relationship. With acute fish data, strong relationships are obtained for all mode of action. <i>Daphnia</i> was found to be more sensitive than fish to several aniline derivatives and pesticides acting through cholinesterase inhibition, and less sensitive than fish to known endocrine disruptors. Extreme (i.e. &lt;1 or &gt;100) interspecies sensitivity ratios were mainly evident for chemicals acting by polar narcosis and specific reactivity. The safety factor of 100 commonly applied in environmental risk assessment does not seem to be equally protective for each mode of action.
DOI: 10.6084/m9.figshare.4224219
title: Two decades of ecohydraulics: trends of an emerging interdiscipline

description: We assessed how the emerging field of ecohydraulics research has changed over two decades by examining the proceedings of the biennial International Symposium on Ecohydraulics. By using Natural Language Processing (NLP) in word usage, this paper provides a deep analysis of a longitudinal dataset and enables us to test more detailed questions than previous snapshots of the ecohydraulics literature. We formulated three main hypotheses related to the degree of multidisciplinarity, interdisciplinarity and transdisciplinarity within ecohydraulics. We investigated temporal changes in author affiliation patterns and identified dominant topics of research. The total number of proceeding papers has increased over time and the field is becoming increasingly global. This and the identification of 10 distinctive macro-topics suggest well-developed multidisciplinarity in ecohydraulics. There has been reasonable stability in individual topics across time, except for 11 (out of 51) significant trends within the macro-topics of <i>Fish responses, Hydraulic modelling, Water quality, Physical habitat modelling</i> and <i>Social responses</i>, suggesting some increase in interdisciplinarity. The proportion of practitioners collaborating with researchers has surprisingly not changed greatly over time, indicating ecohydraulics has been transdisciplinary to some extent from its inception. Our results arguably provide an opportunity to better integrate fundamental understanding into practical applications in water management.
DOI: 10.6084/m9.figshare.4224219.v1
title: Two decades of ecohydraulics: trends of an emerging interdiscipline

description: We assessed how the emerging field of ecohydraulics research has changed over two decades by examining the proceedings of the biennial International Symposium on Ecohydraulics. By using Natural Language Processing (NLP) in word usage, this paper provides a deep analysis of a longitudinal dataset and enables us to test more detailed questions than previous snapshots of the ecohydraulics literature. We formulated three main hypotheses related to the degree of multidisciplinarity, interdisciplinarity and transdisciplinarity within ecohydraulics. We investigated temporal changes in author affiliation patterns and identified dominant topics of research. The total number of proceeding papers has increased over time and the field is becoming increasingly global. This and the identification of 10 distinctive macro-topics suggest well-developed multidisciplinarity in ecohydraulics. There has been reasonable stability in individual topics across time, except for 11 (out of 51) significant trends within the macro-topics of <i>Fish responses, Hydraulic modelling, Water quality, Physical habitat modelling</i> and <i>Social responses</i>, suggesting some increase in interdisciplinarity. The proportion of practitioners collaborating with researchers has surprisingly not changed greatly over time, indicating ecohydraulics has been transdisciplinary to some extent from its inception. Our results arguably provide an opportunity to better integrate fundamental understanding into practical applications in water management.
DOI: 10.6084/m9.figshare.4224216
title: Supplementary Material for: Occurrence and Origin of Supernumerary Chromosomes in Partamona (Hymenoptera: Apidae: Meliponini)

description: Samples from 861 colonies of 12 <i>Partamona</i> species from 125 Brazilian localities were analysed for a SCAR marker specific to the B chromosomes of <i>P. helleri</i>. We identified the SCAR marker in 6 of the 12 species analysed, including 2 <i>(P. gregaria</i> and <i>P. chapadicola)</i> from the pearsoni clade. This is the first report on the presence of this marker in <i>Partamona</i> species that are not included in the cupira clade, which indicates that the B chromosomes probably are more widespread in this genus than previously thought. The analysis revealed a high frequency of the SCAR marker in the samples of <i>P. helleri</i> (0.47), <i>P. cupira</i> (0.46), and <i>P. rustica</i> (0.29), and a low frequency in <i>P.</i> aff.<i>helleri</i> (0.06). The frequency of the marker in <i>P. helleri</i> was correlated with the latitude of the sampling locality, decreasing from north to south. Sequence data on the SCAR marker from 50 individuals of the 6 species in which the presence of this marker was shown revealed a new scenario for the origin of the B chromosomes in <i>Partamona</i>.
DOI: 10.6084/m9.figshare.4224228.v1
title: part01.zip

description: raw data of the tomography of teeth (part 1)<br>
DOI: 10.6084/m9.figshare.4224216.v1
title: Supplementary Material for: Occurrence and Origin of Supernumerary Chromosomes in Partamona (Hymenoptera: Apidae: Meliponini)

description: Samples from 861 colonies of 12 <i>Partamona</i> species from 125 Brazilian localities were analysed for a SCAR marker specific to the B chromosomes of <i>P. helleri</i>. We identified the SCAR marker in 6 of the 12 species analysed, including 2 <i>(P. gregaria</i> and <i>P. chapadicola)</i> from the pearsoni clade. This is the first report on the presence of this marker in <i>Partamona</i> species that are not included in the cupira clade, which indicates that the B chromosomes probably are more widespread in this genus than previously thought. The analysis revealed a high frequency of the SCAR marker in the samples of <i>P. helleri</i> (0.47), <i>P. cupira</i> (0.46), and <i>P. rustica</i> (0.29), and a low frequency in <i>P.</i> aff.<i>helleri</i> (0.06). The frequency of the marker in <i>P. helleri</i> was correlated with the latitude of the sampling locality, decreasing from north to south. Sequence data on the SCAR marker from 50 individuals of the 6 species in which the presence of this marker was shown revealed a new scenario for the origin of the B chromosomes in <i>Partamona</i>.
DOI: 10.6084/m9.figshare.4224210
title: Multiple Locus Genome-wide Association Studies for Important Economic Traits of Oil Palm

description: These are the raw data analyzed in the paper entitled “Multiple Locus Genome-wide Association Studies for Important Economic Traits of Oil Palm”. The file has two sheets. The first sheet stores the genotype data consisted of 1081 SNPs from the 422 oil palms. The second sheet named “phenotype” is the field data of 13 traits.
DOI: 10.6084/m9.figshare.4224228.v3
title: Mass density measurement of mineralized tissue with grating-based x-ray phase tomography

description: raw synchrotron data of a grating-based X-ray phase tomography of teeth <br>
DOI: 10.6084/m9.figshare.4224228.v2
title: phase contrast tomography scan of teeth

description: raw data of the tomography of teeth <br>
DOI: 10.6084/m9.figshare.4224204
title: Using the Three Delays Model to Examine Civil Registration in Indonesia Raw Data.zip

description: This project demonstrates the applicability of the Three Delays Model to Indonesia's civil registration system and examines how efforts to strengthen civil registration services can draw on lessons from maternal and child health programming. 20 focus group discussions (FGDs) were conducted using a participatory ranking exercise in four Indonesian districts. FGDs were stratified into four groups: (1) government officials involved in civil registration, (2) civil society organization members that assist communities in civil registration, and (3) female and (4) male community members. This repository houses all of the raw transcripts for the project. The participant names have been de-identified to preserve their confidentiality. The study objectives and details about the FGD sessions were explained to all participants, and their informed consent to participate and be recorded were received before the recording began. A glossary is provided to explain all initializations.
DOI: 10.6084/m9.figshare.4224207
title: Supplementary Material for: Cell-Derived Microparticles in Patients with Type 2 Diabetes Mellitus: a Systematic Review and Meta-Analysis

description: <i>Background/Aims: </i>The aim of this study was to assess the association between circulating cell-derived microparticles (MPs) and type 2 diabetes mellitus (T2DM). <i>Methods: </i>A literature search was performed systematically in PubMed and Embase to identify available case-control or cross-sectional studies that compared different types of cell-derived MPs in patients with T2DM and non-diabetic controls. Pooled standardized mean differences (SMDs) of each MP type were pooled using meta-analysis. <i>Results: </i>Forty-eight studies involving 2,460 patients with T2DM and 1,880 non-diabetic controls were included for systematic review and 34 of which were included for quantitative study by meta-analysis. In the overall analysis, the levels of circulating total MPs (TMPs), platelet-derived MPs (PMPs), monocyte-derived MPs (MMPs) and endothelium-derived MPs (EMPs) were significantly higher in T2DM patients than those in controls (TMPs: SMD, 0.64; 95%CI, 0.12∼1.15; P=0.02; PMPs: SMD, 1.19; 95%CI, 0.88∼1.50; P &lt;0.00001; MMPs: SMD, 0.92; 95%CI, 0.66∼1.17; P &lt;0.00001; EMPs: SMD, 0.73; 95%CI, 0.50∼0.96; P &lt;0.00001). Meanwhile, no significant difference was shown in leukocyte-derived MPs (LMPs) level between diabetic and non-diabetic groups (SMD, 0.37; 95%CI, -0.15∼0.89; P=0.17). <i>Conclusions: </i>The counts of TMPs, PMPs, MMPs and EMPs elevated in patients with T2DM. And cell-derived MPs may play a role in the pathogenesis of T2DM.
DOI: 10.6084/m9.figshare.4224204.v2
title: Using the Three Delays Model to Examine Civil Registration in Indonesia Raw Data.zip

description: This project demonstrates the applicability of the Three Delays Model to Indonesia's civil registration system and examines how efforts to strengthen civil registration services can draw on lessons from maternal and child health programming. 20 focus group discussions (FGDs) were conducted using a participatory ranking exercise in four Indonesian districts. FGDs were stratified into four groups: (1) government officials involved in civil registration, (2) civil society organization members that assist communities in civil registration, and (3) female and (4) male community members. This repository houses all of the raw transcripts for the project. The participant names have been de-identified to preserve their confidentiality. The study objectives and details about the FGD sessions were explained to all participants, and their informed consent to participate and be recorded were received before the recording began. A glossary is provided to explain all initializations.
DOI: 10.6084/m9.figshare.4224204.v1
title: Using the Three Delays Model to Examine Civil Registration in Indonesia Raw Data.zip

description: This project demonstrates the applicability of the Three Delays Model to Indonesia's civil registration system and examines how efforts to strengthen civil registration services can draw on lessons from maternal and child health programming. 20 focus group discussions (FGDs) were conducted using a participatory ranking exercise in four Indonesian districts. FGDs were stratified into four groups: (1) government officials involved in civil registration, (2) civil society organization members that assist communities in civil registration, and (3) female and (4) male community members. This repository houses all of the raw transcripts for the project. The participant names have been de-identified to preserve their confidentiality. The study objectives and details about the FGD sessions were explained to all participants, and their informed consent to participate and be recorded were received before the recording began. A glossary is provided to explain all initializations.
DOI: 10.6084/m9.figshare.4224192
title: Twelve tips for turning quality assurance data into undergraduate teaching awards: A quality improvement and student engagement initiative

description: Data on teaching awards in undergraduate medical education are sparse. The benefits of an awards system may seem obvious at first glance. However, there are also potential problems relating to fairness, avoidance of bias, and alignment of the awards system with a wider strategy for quality improvement and curriculum development. Here, we report five- year single center experience with establishing undergraduate teaching awards in a large academic teaching hospital. Due to lack of additional funding we based our awards not on peer review but mainly on existing and very comprehensive quality assurance (QA) data. Our 12 tips describe practical points but also pitfalls with awards categories and criteria, advertising and disseminating the awards, the actual awards ceremony and finally embedding the awards in the hospital’s wider strategy. To be truly successful, teaching awards and prizes need to be carefully considered, designed and aligned with a wider institutional strategy of rewarding enthusiastic educators.