cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3659463
title: Patterns of failure following post-operative intensity-modulated radiotherapy in oral cavity cancer: Planning CT and Recurrence CT dataset

description: <i>Purpose of Original Study</i>We sought to identify spatial/dosimetric patterns of failure for oral cavity cancer (OCC) patients receiving post-operative intensity-modulated radiotherapy (PO-IMRT).<i>Material and Methods</i>289 OCC patients receiving PO-IMRT from a single institution were retrospectively reviewed from 2000-2012 with institutional review board approval. Diagnostic CT/PET-CT documenting recurrence (rCT) was co-registered with original planning CTs (pCT) using a validated deformable image registration (DIR) workflow. Manually segmented recurrent gross disease (rGTV) on rCT was deformed to co-registered pCTs. Mapped rGTVs were compared dosimetrically to planned dose and spatially to original planning target volumes (TVs) using centroid-based approaches. Technical details for the DIR workflow methodology are found in the references below.We classify failure using standardized institutional classification system combining spatial/dosimetric criteria: A (central high dose), B (peripheral high dose), C (central elective dose), D (peripheral elective dose), and E (extraneous dose). Definitions of failure classifications are further described in the references below. Of 63 patients with locoregional recurrences, 48 patients had available rCT and pCT for analysis. In this dataset of 48 patient rCTs, 75 rGTVs were identified.<i>Purpose of Sharing Anonymized Dataset</i>We hope that by utilizing a standardized typology for reporting patterns of failure in OCC following PO-IMRT, which can be adopted by multiple institutions, we can encourage other comparable reporting practices for PO-IMRT, in a manner that allows improved detection of possible modes of preventable error; for this reason, we are posting an anonymized archive of the extant dataset via digital repository.In this anonymized fileset in DICOM format, we share the following:1. Original pCTs of 48 patients, along with original planning TVs2. Prescribed dose to original pCTs 3. rCTs of 48 patients, along with the 75 rGTVs
DOI: 10.6084/m9.figshare.3659463.v1
title: Patterns of failure following post-operative intensity-modulated radiotherapy in oral cavity cancer: Planning CT and Recurrence CT dataset

description: <i>Purpose of Original Study</i>We sought to identify spatial/dosimetric patterns of failure for oral cavity cancer (OCC) patients receiving post-operative intensity-modulated radiotherapy (PO-IMRT).<i>Material and Methods</i>289 OCC patients receiving PO-IMRT from a single institution were retrospectively reviewed from 2000-2012 with institutional review board approval. Diagnostic CT/PET-CT documenting recurrence (rCT) was co-registered with original planning CTs (pCT) using a validated deformable image registration (DIR) workflow. Manually segmented recurrent gross disease (rGTV) on rCT was deformed to co-registered pCTs. Mapped rGTVs were compared dosimetrically to planned dose and spatially to original planning target volumes (TVs) using centroid-based approaches. Technical details for the DIR workflow methodology are found in the references below.We classify failure using standardized institutional classification system combining spatial/dosimetric criteria: A (central high dose), B (peripheral high dose), C (central elective dose), D (peripheral elective dose), and E (extraneous dose). Definitions of failure classifications are further described in the references below. Of 63 patients with locoregional recurrences, 48 patients had available rCT and pCT for analysis. In this dataset of 48 patient rCTs, 75 rGTVs were identified.<i>Purpose of Sharing Anonymized Dataset</i>We hope that by utilizing a standardized typology for reporting patterns of failure in OCC following PO-IMRT, which can be adopted by multiple institutions, we can encourage other comparable reporting practices for PO-IMRT, in a manner that allows improved detection of possible modes of preventable error; for this reason, we are posting an anonymized archive of the extant dataset via digital repository.In this anonymized fileset in DICOM format, we share the following:1. Original pCTs of 48 patients, along with original planning TVs2. Prescribed dose to original pCTs 3. rCTs of 48 patients, along with the 75 rGTVs
DOI: 10.6084/m9.figshare.3659067
title: Functional MHC-distances between reed warbler females and their social and EPP mates.xlsx

description: Dataset provided as a part of the publication "Female reed warblers increase MHC allelic divergence in offspring through extra-pair copulations" by Halupka et al.<strong></strong>
DOI: 10.6084/m9.figshare.3659067.v1
title: Functional MHC-distances between reed warbler females and their social and EPP mates.xlsx

description: Dataset provided as a part of the publication "Female reed warblers increase MHC allelic divergence in offspring through extra-pair copulations" by Halupka et al.<strong></strong>
DOI: 10.6084/m9.figshare.3652344
title: Caprine PrP variants harboring Asp-146, His-154 and Gln-211 alleles display reduced convertibility upon interaction with pathogenic murine prion protein in scrapie infected cells

description: Scrapie, the prion disease of sheep and goats, is a devastating malady of small ruminants. Due to its infectious nature, epidemic outbreaks may occur in flocks/herds consisting of highly susceptible animals. Field studies identified scrapie-protective caprine PrP variants, harboring specific single amino acid changes (Met-142, Arg-143, Asp-146, Ser-146, His-154, Gln-211 and Lys-222). Their effects are under further evaluation, and aim to determine the most protective allele. We assessed some of these variants (Asp-146, His-154, Gln-211 and Lys-222), after their exogenous expression as murine-caprine chimeras in a scrapie- infected murine cell line. We report that exogenously expressed PrPs undergo conformational conversion upon interaction with the endogenous pathological murine prion protein (PrP<sup>SC</sup>), which results in the detection of goat-specific and partially PK-resistant moieties. These moieties display a PK-resistance pattern distinct from the one detected in natural goat scrapie cases. Within this cellular model, distinct conformational conversion potentials were assigned to the tested variants. Molecules carrying the Asp-146, His-154 and Gln-211 alleles showed significantly lower conversion levels compared to wild type, confirming their protective effects against scrapie. Although we utilized a heterologous conversion system, this is to our knowledge, the first study of caprine PrP variants in a cellular context of scrapie, that confirms the protective effects of some of the studied alleles.
DOI: 10.6084/m9.figshare.3652344.v1
title: Caprine PrP variants harboring Asp-146, His-154 and Gln-211 alleles display reduced convertibility upon interaction with pathogenic murine prion protein in scrapie infected cells

description: Scrapie, the prion disease of sheep and goats, is a devastating malady of small ruminants. Due to its infectious nature, epidemic outbreaks may occur in flocks/herds consisting of highly susceptible animals. Field studies identified scrapie-protective caprine PrP variants, harboring specific single amino acid changes (Met-142, Arg-143, Asp-146, Ser-146, His-154, Gln-211 and Lys-222). Their effects are under further evaluation, and aim to determine the most protective allele. We assessed some of these variants (Asp-146, His-154, Gln-211 and Lys-222), after their exogenous expression as murine-caprine chimeras in a scrapie- infected murine cell line. We report that exogenously expressed PrPs undergo conformational conversion upon interaction with the endogenous pathological murine prion protein (PrP<sup>SC</sup>), which results in the detection of goat-specific and partially PK-resistant moieties. These moieties display a PK-resistance pattern distinct from the one detected in natural goat scrapie cases. Within this cellular model, distinct conformational conversion potentials were assigned to the tested variants. Molecules carrying the Asp-146, His-154 and Gln-211 alleles showed significantly lower conversion levels compared to wild type, confirming their protective effects against scrapie. Although we utilized a heterologous conversion system, this is to our knowledge, the first study of caprine PrP variants in a cellular context of scrapie, that confirms the protective effects of some of the studied alleles.
DOI: 10.6084/m9.figshare.3652188
title: Intra-host mathematical model of chronic wasting disease dynamics in deer (<i>Odocoileus</i>)

description: Bioassays of native cervid hosts have established the presence of infectious chronic wasting disease (CWD) prions in saliva, blood, urine, and feces of clinically diseased and pre-clinical infected deer. The intra-host trafficking of prions from the time of initial infection to shedding has been less well defined. We created a discrete-time compartmentalized model to simulate the misfolding catalysis, trafficking, and shedding of infectious prions throughout the organ systems of CWD-infected cervids. Using parameter values derived from experimental infections of North American deer (<i>Odocoileus spp</i>.), the exponential-based model predicts prion deposition over time with: 1) nervous tissues containing the highest deposition of prions at 20 months post-infection and 2) excreted fluids containing low levels of prions throughout infection with the highest numbers of prions predicted to be shed in saliva and feces (as high as 10 lethal doses (1.34 × 10<sup>29</sup> prions) in 11–15 months). These findings are comparable to prion deposition described in literature as assayed by conventional and ultrasensitive amplification assays. The comparison of our model to published data suggests that highly sensitive assays (sPMCA, RT-QuIC, and bioassay) are appropriate for early prion detection in bodily fluids and secretions. The model provides a view of intra-host prion catalysis leading to pre-clinical shedding and provides a framework for continued development of antemortem diagnostic methods.
DOI: 10.6084/m9.figshare.3652188.v1
title: Intra-host mathematical model of chronic wasting disease dynamics in deer (<i>Odocoileus</i>)

description: Bioassays of native cervid hosts have established the presence of infectious chronic wasting disease (CWD) prions in saliva, blood, urine, and feces of clinically diseased and pre-clinical infected deer. The intra-host trafficking of prions from the time of initial infection to shedding has been less well defined. We created a discrete-time compartmentalized model to simulate the misfolding catalysis, trafficking, and shedding of infectious prions throughout the organ systems of CWD-infected cervids. Using parameter values derived from experimental infections of North American deer (<i>Odocoileus spp</i>.), the exponential-based model predicts prion deposition over time with: 1) nervous tissues containing the highest deposition of prions at 20 months post-infection and 2) excreted fluids containing low levels of prions throughout infection with the highest numbers of prions predicted to be shed in saliva and feces (as high as 10 lethal doses (1.34 × 10<sup>29</sup> prions) in 11–15 months). These findings are comparable to prion deposition described in literature as assayed by conventional and ultrasensitive amplification assays. The comparison of our model to published data suggests that highly sensitive assays (sPMCA, RT-QuIC, and bioassay) are appropriate for early prion detection in bodily fluids and secretions. The model provides a view of intra-host prion catalysis leading to pre-clinical shedding and provides a framework for continued development of antemortem diagnostic methods.
DOI: 10.21223/vxo3lc/i9w9jf
title: DataDictionary_Introduction.csv

description: :unav
DOI: 10.21223/vxo3lc/mofnfh
title: 12538_PTYield062018_HOLE_exp1.tab
DOI: 10.21223/vxo3lc/opetts
title: 12538_DataDictionary_ElementDescripti.xlsx

description: :unav
DOI: 10.21223/vxo3lc/bijlz3
title: 12538_DataDictionary_UniqueIdentifier.xls

description: :unav
DOI: 10.21223/vxo3lc/njnewg
title: 12538_PTYield062018_HOLE_exp1.tab

description: :unav
DOI: 10.21223/vxo3lc/hrdqwy
title: 12538_PTYield062018_HOLE_exp1.tab
DOI: 10.21223/vxo3lc/2cmnhi
title: 12538_PTYield062018_HOLE_exp1.tab
DOI: 10.21223/vxo3lc/h3xvsp
title: 12538_PTYield062018_HOLE_exp1.tab
DOI: 10.6084/m9.figshare.3649023
title: Table2.csv

description: Table2 contains high frequency (12-96kHz) acoustic information created by AudioTagger (https://github.com/groakat/AudioTagger) and acoustic indices calculated in R using the 'soundecology' package v.1.1.1.
DOI: 10.6084/m9.figshare.3649023.v1
title: Table2.csv

description: Table2 contains high frequency (12-96kHz) acoustic information created by AudioTagger (https://github.com/groakat/AudioTagger) and acoustic indices calculated in R using the 'soundecology' package v.1.1.1.
DOI: 10.6084/m9.figshare.3644991
title: Classifying Interdisciplinary Research in Scholars@TAMU

description: Texas A&M University (TAMU) recently identified six interdisciplinary and societally-relevant research themes as strengths of the institution that address societal grand challenges.<br>TAMU Libraries are interested in adapting and extending the VIVO ontology in order to create a dashboard that represents research products (i.e., manuscripts and grants), accomplishments, and the communities addressing each of these themes.<br>This would support and demonstrate TAMU’s societal impact.<br>This poster presents a plan for the experimental classification of multidisciplinary research studies.
DOI: 10.6084/m9.figshare.3644991.v2
title: Classifying Interdisciplinary Research in Scholars@TAMU

description: Texas A&M University (TAMU) recently identified six interdisciplinary and societally-relevant research themes as strengths of the institution that address societal grand challenges.<br>TAMU Libraries are interested in adapting and extending the VIVO ontology in order to create a dashboard that represents research products (i.e., manuscripts and grants), accomplishments, and the communities addressing each of these themes.<br>This would support and demonstrate TAMU’s societal impact.<br>This poster presents a plan for the experimental classification of multidisciplinary research studies.
DOI: 10.6084/m9.figshare.3644847
title: Supplementary Material for: Geographical Variation in Dementia Mortality in Italy, New Zealand, and Chile: The Impact of Latitude, Vitamin D, and Air Pollution

description: <b><i>Background:</i></b> Dementia risk is reported as being higher in the north compared to the south, which may be related to vitamin D deficiency. If this were the case, an opposite gradient of risk would be observed in the southern hemisphere, but this has not been investigated previously. <b><i>Methods:</i></b> We calculated standardised mortality ratios (SMRs) for deaths in 2012 where dementia (Alzheimer's disease, vascular or unspecified dementia) was recorded as the underlying cause for 20 regions in Italy, 20 District Health Board areas in New Zealand and 29 Health Service areas in Chile. <b><i>Results:</i></b> Dementia SMRs were higher in northern than central or southern Italy. The inverse pattern was seen in women in New Zealand, with rates higher on South Island than North Island. However, dementia risk was raised in eight regions in the north and centre of Chile in both men and women. <b><i>Conclusions:</i></b> Geographical variation plays a key role in dementia risk, but patterns vary in men and women. In the northern hemisphere, dementia mortality is higher in the north, but the pattern in the southern hemisphere is more complex.
DOI: 10.6084/m9.figshare.3644553
title: Supplementary Material for: Adverse Events Following International Normalized Ratio Reversal in Intracerebral Hemorrhage

description: <b><i>Background:</i></b> Prothrombin complex concentrates (PCCs) are frequently used to reverse the effect of vitamin K antagonists (VKAs) in patients with non-traumatic intracerebral hemorrhage (ICH). However, information on the rate of thromboembolic events (TEs) and allergic events after PCC therapy in VKA-ICH patients is limited. <b><i>Methods:</i></b> Consecutive VKA-ICH patients treated with PCC at our institution between December 2004 and June 2014 were included into this retrospective observational study. We recorded international normalized ratio (INR) values before and after PCC treatment, baseline clinical characteristics including the premorbid modified Rankin Scale (pmRS) score, TE and allergic event that occurred during the hospital stay. All events were classified by 3 reviewers as being ‘related', ‘probably related', ‘possibly related', ‘unlikely related' or ‘not related' to treatment with PCC. To identify factors associated with TEs, log-rank analyses were applied. <b><i>Results:</i></b> Two hundred and five patients were included. Median INR was 2.8 (interquartile range (IQR) 2.2-3.8) before and 1.3 (IQR 1.2-1.4) after PCC treatment and a median of 1,500 IU PCC (IQR 1,000-2,500) was administered. Nineteen TEs were observed (9.3%); none were classified ‘related' but 9 were classified as ‘possibly' or ‘probably related' to PCC infusion (4.4%). One allergic reaction (0.5%), ‘unlikely related' to PCC, was observed. In the whole cohort, PCC doses &gt;2,000-3,000 IU, ICH volumes &gt;40 ml, National Institute of Health Stroke Scale values &gt;10 and a pmRS &gt;2 were associated with the development of TEs (p = 0.031, p = 0.034, p = 0.050 and p = 0.036, respectively). <b><i>Conclusions:</i></b> Overall, INR reversal with PCC appears safe. Though no clear relationship between higher PCC dosing and TEs was observed, PCC doses between &gt;2,000 and 3,000 IU and higher morbidity at ICH onset were associated with TEs. Hence, individual titration of PCC to avoid exposure to unnecessarily high doses using point-of-care devices should be prospectively explored.<br>
DOI: 10.6084/m9.figshare.3637833
title: Bi-ventricular interplay in patients with systemic sclerosis-associated pulmonary arterial hypertension: Detection by cardiac magnetic resonance

description: <i>Objectives</i>: Pulmonary arterial hypertension (PAH) associated with systemic sclerosis (SSc) has a poor prognosis compared to PAH associated with other connective tissue diseases (CTD). The objective of this study was to examine the difference in hemodynamic state between SSc-PAH and other CTD-PAH by performing cardiac magnetic resonance (CMR) imaging. <i>Methods</i>: A single center retrospective analysis was conducted comprising 40 consecutive CTD patients who underwent right heart catheterization and CMR at the same period from January 2010 to October 2015. <i>Results</i>: Thirty-two patients had pre-capillary pulmonary hypertension. Of these, 15 had SSc and 17 had other CTD. CMR measurements, particularly the ratio of right to left end-diastolic volume (RVEDV/LVEDV), correlated well with mean pulmonary arterial pressure (mPAP). Conversely, RVEDV/LVEDV and mPAP correlated differently in SSc and non-SSc patients. In SSc patients, the ratio of RVEDV/LVEDV to mPAP was significantly higher compared to non-SSc patients. In the follow-up study, 2 SSc patients exhibited increased RVEDV/LVEDV in spite of decreased mPAP following treatment. Kaplan–Meier analysis revealed poor prognosis of patients with increased RVEDV/LVEDV following treatment. <i>Conclusions</i>: Our data indicated that altered bi-ventricular interplay detected at CMR may represent SSc-related cardiac involvement and reflect poor prognosis of SSc-PAH.
DOI: 10.6084/m9.figshare.3637833.v2
title: Bi-ventricular interplay in patients with systemic sclerosis-associated pulmonary arterial hypertension: Detection by cardiac magnetic resonance

description: <i>Objectives</i>: Pulmonary arterial hypertension (PAH) associated with systemic sclerosis (SSc) has a poor prognosis compared to PAH associated with other connective tissue diseases (CTD). The objective of this study was to examine the difference in hemodynamic state between SSc-PAH and other CTD-PAH by performing cardiac magnetic resonance (CMR) imaging. <i>Methods</i>: A single center retrospective analysis was conducted comprising 40 consecutive CTD patients who underwent right heart catheterization and CMR at the same period from January 2010 to October 2015. <i>Results</i>: Thirty-two patients had pre-capillary pulmonary hypertension. Of these, 15 had SSc and 17 had other CTD. CMR measurements, particularly the ratio of right to left end-diastolic volume (RVEDV/LVEDV), correlated well with mean pulmonary arterial pressure (mPAP). Conversely, RVEDV/LVEDV and mPAP correlated differently in SSc and non-SSc patients. In SSc patients, the ratio of RVEDV/LVEDV to mPAP was significantly higher compared to non-SSc patients. In the follow-up study, 2 SSc patients exhibited increased RVEDV/LVEDV in spite of decreased mPAP following treatment. Kaplan–Meier analysis revealed poor prognosis of patients with increased RVEDV/LVEDV following treatment. <i>Conclusions</i>: Our data indicated that altered bi-ventricular interplay detected at CMR may represent SSc-related cardiac involvement and reflect poor prognosis of SSc-PAH.
DOI: 10.6084/m9.figshare.3636990
title: Supplementary Material for: Contribution of IVIM to Conventional Dynamic Contrast-Enhanced and Diffusion-Weighted MRI in Differentiating Benign from Malignant Breast Masses

description: <b><i>Background:</i></b> The aim of this study was to determine whether the indicators obtained from intravoxel incoherent motion (IVIM) imaging can improve the characterization of benign and malignant breast masses compared with conventional dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and diffusion-weighted magnetic resonance imaging (DW-MRI). <b><i>Patients and Methods:</i></b> This study included 23 benign and 31 malignant breast masses of 48 patients. Main indicators were initial enhancement ratio (IER), time-signal intensity curve (TIC), apparent diffusion coefficient (ADC), tissue diffusivity (D), pseudodiffusivity (D*), and perfusion fraction (f). The discriminative abilities of the different models were compared by means of receiver operating characteristic (ROC) curve and area under the ROC curve (AUC) analysis. <b><i>Results:</i></b> D had the highest AUC (0.980), sensitivity (93.55%), specificity (100%), and diagnostic accuracy (96.36%). Both D and TIC could provide the independent predicted features for malignant breast masses. The combination of D and TIC had an AUC of up to 0.990. <b><i>Conclusion:</i></b> D of IVIM can effectively complement existing conventional DCE-MRI and DW-MRI in differentiating malignant from benign breast masses. IVIM combined with DCE-MRI is a robust means of evaluating breast masses.