cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5612086.v1
title: Supplementary Material for: Survival Outcome of Intermediate-Grade Salivary Gland Carcinoma

description: <b><i>Objective:</i></b> Histological grade is the most important factor for defining treatment strategies and predicting prognosis for salivary gland carcinoma (SGC). We examined factors affecting long-term recurrence and survival among intermediate-grade SGC (IGSGC) patients to define optimal treatment modalities and outcomes. <b><i>Methods:</i></b> We reviewed the clinical and pathological data on 108 IGSGC patients who underwent definitive surgery with or without postoperative radiotherapy. We compared treatment outcomes by treatment strategies such as surgical extent for the primary tumor, neck dissection, or postoperative radiotherapy. <b><i>Results:</i></b> During a 103-month median follow-up, local, regional, and distant recurrences were detected in 14 (13.0%), 3 (2.8%), and 21 (19.4%) patients, respectively. The 10-year locoregional control (LRC), distant metastasis-free survival (DMFS), and overall survival (OS) rates were 83.1, 76.0, and 80.1%, respectively. Multivariate analyses identified a nonparotid primary site as an independent prognostic factor for LRC (<i>p</i> = 0.018). Adenoid cystic carcinoma and a positive pN classification were significantly unfavorable prognostic factors for DMFS (<i>p</i> = 0.025 and <i>p</i> = 0.030, respectively); overall advanced stage was an independent prognostic factor for OS (<i>p</i> = 0.020). Surgical extent, elective neck dissection, and postoperative adjuvant radiotherapy did not significantly affect treatment outcomes. <b><i>Conclusion:</i></b> Patients with early-stage IGSGC of parotid origin can achieve favorable treatment outcomes with conservative surgery alone.
DOI: 10.6084/m9.figshare.5612680.v1
title: Response of rumen bacterial diversity and fermentation parameters in beef cattle to diets containing supplemental daidzein

description: An experiment was conducted to determine the effects of soy isoflavone daidzein on ruminal fermentation, microbial protein synthesis and rumen bacterial community in beef cattle. Six rumen-cannulated adult beef cattle were assigned to three blocks according to similar body weight in a randomised block design, with two cattle each block. Each block randomly received one of the two dietary treatments: control (basal concentrate) and daidzein (supplementation with 500 mg daidzein/kg basal concentrate). High-throughput sequencing data showed that supplemental daidzein increased the relative abundance of bacteria belonging to phylum Bacteroidetes (<i>p</i> = .050), but reduced and tended to reduce the relative abundance of phylum Spirochaetae (<i>p</i> = .030) and Firmicutes (<i>p</i> = .080). At the genus level, the relative abundance of <i>Prevotella</i> (<i>p</i> = .036), <i>RC9_gut_group</i> (<i>p</i> = .019), <i>Succinivibrio</i> (<i>p</i> = .093) and <i>Ruminobacter</i> (<i>p</i> = .085) were increased or tended to be increased by daidzein supplementation. However, supplemental daidzein reduced or tended to reduce some uncultured and unclassified bacteria genus belonging to <i>Ruminococcaceae</i> (<i>p</i> = .028), <i>Prevotellaceae</i> (<i>p</i> = .088) and <i>Lachnospiraceae</i> (<i>p</i> = .068). The ruminal pH (<i>p</i> = .023) and ammonia-N (<i>p</i> = .031) concentration were lower in the daidzein group than in the control group, but the daidzein group tended to have greater ruminal total VFA (<i>p</i> = .063) concentration. Supplemental daidzein increased urinary excretion of allantoin (<i>p</i> = .005) and total purine derivatives (<i>p</i> = .007). Current results suggest that supplemental daidzein can affect ruminal fermentation by changing ruminal microbial community, increase the production of VFA and enhance microbial protein synthesis in the rumen, showing the potential of daidzein for improving ruminal fermentation in beef cattle.
DOI: 10.6084/m9.figshare.5612083
title: Dataset for: A framework for ecological risk assessment of metal mixtures in aquatic systems

description: Although metal mixture toxicity has been studied relatively intensely, there is no general consensus yet on how to incorporate metal mixture toxicity into aquatic risk assessment. Here, we combined existing data on chronic metal mixture toxicity at the species level with species-sensitivity-distribution (SSD)-based in-silico metal mixture risk predictions at the community-level for mixtures of Ni, Zn, Cu, Cd and Pb, in order to develop a tiered risk assessment scheme for metal mixtures in freshwater. Generally, independent action (IA) predicts chronic metal mixture toxicity at the species level most accurately, while concentration addition (CA) is the most conservative model. Mixture effects are non-interactive in 69% (IA) and 44% (CA) and antagonistic in 15% (IA) and 51% (CA) of the experiments, while synergisms are only observed in 15% (IA) and 5% (CA) of the experiments. At low effect sizes (around 10% mixture effect), CA overestimates metal mixture toxicity at the species-level by 1.2-fold (i.e. the Mixture interaction Factor [MiF]; median). Species, metal presence or number of metals does not significantly affect the MiF. To predict metal mixture risk at the community-level, bioavailability-normalization procedures were combined with CA or IA using SSD-techniques in 4 different methods, which were compared using environmental monitoring data of a European river basin (Dommel, the Netherlands). We found that the most simple method, in which CA is directly applied to the SSD (i.e. CASSD), is also the most conservative method. CASSD has a median Margin of Safety (MoS) of 1.1 and 1.2 for binary mixtures relative to the theoretically more consistent methods of applying CA or IA directly to the dose response curve (i.e. CADRC or IADRC, respectively)[...]
DOI: 10.6084/m9.figshare.5612083.v1
title: Dataset for: A framework for ecological risk assessment of metal mixtures in aquatic systems

description: Although metal mixture toxicity has been studied relatively intensely, there is no general consensus yet on how to incorporate metal mixture toxicity into aquatic risk assessment. Here, we combined existing data on chronic metal mixture toxicity at the species level with species-sensitivity-distribution (SSD)-based in-silico metal mixture risk predictions at the community-level for mixtures of Ni, Zn, Cu, Cd and Pb, in order to develop a tiered risk assessment scheme for metal mixtures in freshwater. Generally, independent action (IA) predicts chronic metal mixture toxicity at the species level most accurately, while concentration addition (CA) is the most conservative model. Mixture effects are non-interactive in 69% (IA) and 44% (CA) and antagonistic in 15% (IA) and 51% (CA) of the experiments, while synergisms are only observed in 15% (IA) and 5% (CA) of the experiments. At low effect sizes (around 10% mixture effect), CA overestimates metal mixture toxicity at the species-level by 1.2-fold (i.e. the Mixture interaction Factor [MiF]; median). Species, metal presence or number of metals does not significantly affect the MiF. To predict metal mixture risk at the community-level, bioavailability-normalization procedures were combined with CA or IA using SSD-techniques in 4 different methods, which were compared using environmental monitoring data of a European river basin (Dommel, the Netherlands). We found that the most simple method, in which CA is directly applied to the SSD (i.e. CASSD), is also the most conservative method. CASSD has a median Margin of Safety (MoS) of 1.1 and 1.2 for binary mixtures relative to the theoretically more consistent methods of applying CA or IA directly to the dose response curve (i.e. CADRC or IADRC, respectively)[...]
DOI: 10.6084/m9.figshare.5612071
title: Supplementary Material for: Repeated Micro-Trauma of the Penile Tunica Albuginea: A New Animal Model of Peyronie's Disease

description: <b><i>Objectives:</i></b> To compare effects of repairing injured tunica albuginea (PTA) of rat penis by single or repeated local injections of chlorhexidine ethanol (ChE) into the PTA and to establish a new animal model of Peyronie's disease (PD). <b><i>Materials and Methods:</i></b> Forty-two rats were divided into 7 groups. Rats either served as the normal control group with 1-5 injections of 0.9% saline or they received a single injection, 2, 3, 4, or 5 injections of ChE (0.1% chlorhexidine gluconate plus 15% ethanol dissolved in saline); rats in the positive control group were injected with TGF-β1. At 60 days after the last injection, the intracavernous pressure, degree of penile curvature, and histology were evaluated. <b><i>Results:</i></b> Compared with the single injection of the ChE group, we found the following in the repeat ChE injections groups: an increase in the degree of penile curvature, fibrous plaques in the PTA and/or corpus cavernosum, broken elastic fibers, slightly decreased erectile function, and an increased expression of TGF-β1 and αSMA. <b><i>Conclusions:</i></b> Repeated ChE injuries of PTA may lead to fibrosis. This represents an excellent model of PD that involves repeated injections of ChE into the local PTA as well as reveals the pathophysiologic mechanism of PD.
DOI: 10.6084/m9.figshare.5612074.v1
title: Jharkhand project Axshya paper - Dataset in STATA format

description: Data set in Excel format
DOI: 10.6084/m9.figshare.5612029
title: Epidemiological and treatment-related factors contribute to improved outcome of oropharyngeal squamous cell carcinoma in Finland

description: <b>Background:</b> Treatment for oropharyngeal squamous cell carcinoma (OPSCC) has changed, as the proportion of human papilloma virus (HPV)-related disease has increased. We evaluated nationwide information on its management and outcome during the treatment paradigm change period. <b>Methods</b>: We included all patients diagnosed and treated for OPSCC at the five Finnish university hospitals from 2000 to 2009. Patient records and pathology registries provided the clinicopathological data. p16 staining was performed on primary tumor samples of patients who had received treatment with curative intent. <b>Results:</b> A total of 674 patients were diagnosed and treated for OPSCC and the incidence increased along the study period. Of the evaluable tumors 58.5% were p16-positive and the number of p16-positive tumors increased along the years. The treatment was given with curative intent for 600 patients and it was completed in 564. Of them, 47.9% underwent primary surgery and 52.1% received definitive oncological treatment. Also, the treatment protocol changed towards a more oncological approach. Among patients treated with curative intent the five-year overall, disease-specific and disease-free survival rates were 60.1, 71.5 and 57.0%. In multivariate analysis, p16-positivity seemed to relate to reduced disease mortality in lateral and anterior-wall disease. Depending on primary tumor localization, also sex, classes T3–4, presence of regional metastasis and radiotherapy modality had an association with disease mortality. <b>Conclusion:</b> The incidence of p16-positive OPSCC and delivery of definitive oncological treatment increased in Finland during the study period. An improved survival outcome compared with the previous nationwide investigation was observed in this subset of patients.
DOI: 10.6084/m9.figshare.5612029.v1
title: Epidemiological and treatment-related factors contribute to improved outcome of oropharyngeal squamous cell carcinoma in Finland

description: <b>Background:</b> Treatment for oropharyngeal squamous cell carcinoma (OPSCC) has changed, as the proportion of human papilloma virus (HPV)-related disease has increased. We evaluated nationwide information on its management and outcome during the treatment paradigm change period. <b>Methods</b>: We included all patients diagnosed and treated for OPSCC at the five Finnish university hospitals from 2000 to 2009. Patient records and pathology registries provided the clinicopathological data. p16 staining was performed on primary tumor samples of patients who had received treatment with curative intent. <b>Results:</b> A total of 674 patients were diagnosed and treated for OPSCC and the incidence increased along the study period. Of the evaluable tumors 58.5% were p16-positive and the number of p16-positive tumors increased along the years. The treatment was given with curative intent for 600 patients and it was completed in 564. Of them, 47.9% underwent primary surgery and 52.1% received definitive oncological treatment. Also, the treatment protocol changed towards a more oncological approach. Among patients treated with curative intent the five-year overall, disease-specific and disease-free survival rates were 60.1, 71.5 and 57.0%. In multivariate analysis, p16-positivity seemed to relate to reduced disease mortality in lateral and anterior-wall disease. Depending on primary tumor localization, also sex, classes T3–4, presence of regional metastasis and radiotherapy modality had an association with disease mortality. <b>Conclusion:</b> The incidence of p16-positive OPSCC and delivery of definitive oncological treatment increased in Finland during the study period. An improved survival outcome compared with the previous nationwide investigation was observed in this subset of patients.
DOI: 10.6084/m9.figshare.5612047.v1
title: Programme file for analysis in STATA format

description: The programme file contains the commands for calculation of population weighted mean TB indicators and commands related to multilevel model development.<b></b>
DOI: 10.6084/m9.figshare.5612005
title: Supplementary Material for: LncRNA HANR Promotes Tumorigenesis and Increase of Chemoresistance in Hepatocellular Carcinoma

description: <b><i>Background/Aims:</i></b> Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world and the third leading cause of cancer-related death. Critical roles for long non-coding RNAs (lncRNAs) have recently been demonstrated for a variety of cancers, including hepatocellular carcinoma. However, the effect and mechanism of lncRNAs in HCC tumorigenesis and chemoresistance have not been extensively characterized. <b><i>Methods:</i></b> In the current study, we have identified a HCC-expressed lncRNA termed as <i>HANR</i> (HCC associated long non-coding RNA). We identified <i>HANR</i> by microarray analysis and validated its up-regulated expression by quantitative PCR. RNA pull-down and pathway analyses were conducted to evaluate physical and functional interactions with <i>HANR</i>. <i>In vivo</i> experiments were performed to assess tumorigenesis and increase of chemoresistance. In addition, the <i>HANR</i> expression in HCC specimens was detected by FISH. Xenograft and orthotopic mice model was constructed to observe the effect of <i>HANR</i> on tumorigenesis and chemoresistance <i>in vivo</i>. <b><i>Results:</i></b> <i>HANR</i> was demonstrated to be up-regulated in HCC patients and HCC cell lines. Increased <i>HANR</i> expression in HCC predicted short survival of patients. Knock-down of <i>HANR</i> markedly retarded cell proliferation, suppressed HCC xenograft/orthotopic tumor growth, induced apoptosis and enhanced chemosensitivity to doxorubicin, while over-expression of <i>HANR</i> showed the opposite effects. It was found that <i>HANR</i> bind to GSKIP for regulating the phosphorylation of GSK3β in HCC. <b><i>Conclusion:</i></b> Our results demonstrate that <i>HANR</i> contributes to the development of HCC and is a promising therapeutic target for chemosensitization of HCC cells to doxorubicin, which may represent a promising therapeutic target in the future.
DOI: 10.6084/m9.figshare.5612047.v2
title: Jharkhand project Axshya paper - Programme file for analysis in STATA format

description: The programme file contains the commands for calculation of population weighted mean TB indicators and commands related to multilevel model development. <b></b>
DOI: 10.6084/m9.figshare.5611984
title: Teacher pathways.png

description: The diagram illustrates the teacher as the underpinning of the organisational behavior structure within the school and the cause and effect the teacher has on all major components in the education system
DOI: 10.6084/m9.figshare.9894542.v3
title: Test video capture 3rd Version

description: se this form to edit all information related to your data. Please be as descriptive as possible. The file upload is independent from the rest of the form, so you don't need to save an upload. This message will be replaced with helpful tips and suggestions as you begin interacting with the form.
DOI: 10.6084/m9.figshare.5611342
title: Supplemental Data for Premedical SMP Study.xlsx

description: The Premedical SMP Data Collection file contains the responses obtained from the survey that is provided in the supporting information section. The file consists of two spreadsheets: one spreadsheet is for respondents that attended a SMP prior to medical school (SMP Students tab) and one for those that did not (Traditional Students tab).
DOI: 10.6084/m9.figshare.5611342.v1
title: Supplemental Data for Premedical SMP Study.xlsx

description: The Premedical SMP Data Collection file contains the responses obtained from the survey that is provided in the supporting information section. The file consists of two spreadsheets: one spreadsheet is for respondents that attended a SMP prior to medical school (SMP Students tab) and one for those that did not (Traditional Students tab).
DOI: 10.6084/m9.figshare.5611315
title: Dataset for: Controlled pattern imputation for sensitivity analysis of longitudinal binary and ordinal outcomes with nonignorable dropout

description: The controlled imputation method refers to a class of pattern mixture models (PMM) that have been commonly used as sensitivity analyses of longitudinal clinical trials with nonignorable dropout in recent years. These PMMs assume that subjects in the experimental arm after dropout have similar response profiles to the control subjects, or have worse outcomes than otherwise similar subjects who remain on the experimental treatment. In spite of its popularity, the controlled imputation has not been formally developed for longitudinal binary and ordinal outcomes partially due to the lack of a natural multivariate distribution for such endpoints. In this paper, we propose two approaches for implementing the controlled imputation for binary and ordinal data based respectively on the sequential logistic regression and the multivariate probit model. Efficient Markov chain Monte Carlo algorithms are developed for missing data imputation by using the monotone data augmentation (MDA) technique for the sequential logistic regression, and a parameter expanded MDA scheme for the multivariate probit model.We assess the performance of the proposed procedures by simulation and the analysis of a schizophrenia clinical trial, and compare them with the fully conditional specification, last observation carried forward, and baseline observation carried forward imputation methods.
DOI: 10.23641/asha.5611309
title: Differential diagnosis of apraxia of speech (Basilakos et al., 2017)

description: <b>Purpose: </b>Apraxia of speech (AOS) is a consequence of stroke that frequently co-occurs with aphasia. Its study is limited by difficulties with its perceptual evaluation and dissociation from co-occurring impairments. This study examined the classification accuracy of several acoustic measures for the differential diagnosis of AOS in a sample of stroke survivors.<b>Method: </b>Fifty-seven individuals were included (mean age = 60.8 ± 10.4 years; 21 women, 36 men; mean months poststroke = 54.7 ± 46). Participants were grouped on the basis of speech/language testing as follows: AOS-Aphasia (<i>n</i> = 20), Aphasia Only (<i>n</i> = 24), and Stroke Control (<i>n</i> = 13). Normalized Pairwise Variability Index, proportion of distortion errors, voice onset time variability, and amplitude envelope modulation spectrum variables were obtained from connected speech samples. Measures were analyzed for group differences and entered into a linear discriminant analysis to predict diagnostic classification.<b>Results: </b>Out-of-sample classification accuracy of all measures was over 90%. The envelope modulation spectrum variables had the greatest impact on classification when all measures were analyzed together.<b>Conclusions: </b>This study contributes to efforts to identify objective acoustic measures that can facilitate the differential diagnosis of AOS. Results suggest that further study of these measures is warranted to determine the best predictors of AOS diagnosis.<br><b>Supplemental Material S1. </b>Demarcation of vocalic and consonantal boundaries for calculating the normalized Pairwise Variability Index–Vowels (nPVI-V).<br><b>Supplemental Material S2. </b>Narrow transcription codes used to quantify distortion errors.<br><b>Supplemental Material S3. </b>Criteria for preprocessing speech samples for envelope modulation spectrum (EMS) analyses using Adobe Soundbooth.<br><b>Supplemental Material S4.</b> Correlation coefficients for each predictor variable by group.<br><b>Supplemental Material S5. Table S1.</b> Correlations between predictor variables and ASRS scores for the AOS-Aphasia group only.<b><br></b><b>Supplemental Material S6. </b>LDA results with aphasia severity included.<br>Basilakos, A., Yourganov, G., den Ouden, D.-B., Fogerty, D., Rorden, C., Feenaughty, L., & Fridriksson, J. (2017). A multivariate analytic approach to the differential diagnosis of apraxia of speech. <i>Journal of Speech, Language, and Hearing Research, 60, </i>3378–3392<i>. </i>https://doi.org/10.1044/2017_JSLHR-S-16-0443
DOI: 10.6084/m9.figshare.5611315.v1
title: Dataset for: Controlled pattern imputation for sensitivity analysis of longitudinal binary and ordinal outcomes with nonignorable dropout

description: The controlled imputation method refers to a class of pattern mixture models (PMM) that have been commonly used as sensitivity analyses of longitudinal clinical trials with nonignorable dropout in recent years. These PMMs assume that subjects in the experimental arm after dropout have similar response profiles to the control subjects, or have worse outcomes than otherwise similar subjects who remain on the experimental treatment. In spite of its popularity, the controlled imputation has not been formally developed for longitudinal binary and ordinal outcomes partially due to the lack of a natural multivariate distribution for such endpoints. In this paper, we propose two approaches for implementing the controlled imputation for binary and ordinal data based respectively on the sequential logistic regression and the multivariate probit model. Efficient Markov chain Monte Carlo algorithms are developed for missing data imputation by using the monotone data augmentation (MDA) technique for the sequential logistic regression, and a parameter expanded MDA scheme for the multivariate probit model.We assess the performance of the proposed procedures by simulation and the analysis of a schizophrenia clinical trial, and compare them with the fully conditional specification, last observation carried forward, and baseline observation carried forward imputation methods.
DOI: 10.6084/m9.figshare.5611306
title: Matrixes.zip

description: The matrixes datasets used for all phylogenetic analysis.
DOI: 10.6084/m9.figshare.5611303
title: Nest-dismantling

description: Data for nest-dismantling manuscript
DOI: 10.6084/m9.figshare.5611294
title: Enhancing knowledge of head and neck anatomy in preclinical medical students using low fidelity simulation

description: Dataset used in analysis of "Enhancing knowledge of head and neck anatomy in preclinical medical students using low-fidelity simulation"
DOI: 10.6084/m9.figshare.5611303.v1
title: Nest-dismantling

description: Data for nest-dismantling manuscript
DOI: 10.6084/m9.figshare.5611255
title: Short-term gains in histology knowledge: A veterinary gaming application

description: Data set used in manuscript, "Short-term gains in histology knowledge: A veterinary gaming application"