cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5346076.v1
title: Quaternary intertidal and supratidal crabs (Decapoda, Brachyura) from tropical America and the systematic affinities of fossil fiddler crabs

description: Concentrations of fully articulated crabs are rare in the fossil record, especially for terrestrial and semi-terrestrial taxa, which tend to be represented by scarce, fragmentary and poorly preserved fossils due to preservational biases. A newly discovered fossiliferous locality at Bahia Bique, west of Panama City, Panama, yielded a collection of supratidal, intertidal and shallow subtidal invertebrates and vertebrates of mid-Holocene age. Notable discoveries include the first fossils of the sally lightfoot crab <i>Grapsus</i>, the first for the land crab <i>Cardisoma</i> in the Eastern Pacific and, remarkably, the most complete and abundant collection of fossil fiddler crabs, <i>Uca</i>, yet discovered. The abundance and exceptional preservation of fossil male, female, juvenile and adult individuals of <i>Uca</i> aff. <i>ornata</i> in eroded burrow infills suggest that rapid entombment and early diagenesis were crucial for their preservation. The habitat preference of extant <i>U. ornata</i> for soft muds of open intertidal mudflats indicates that part of Bahía Bique must have been a large estuarine mudflat with close proximity to freshwater influx, in contrast to the present-day gravel field where the fossils are found as <i>ex situ</i> boulders, cobbles and gravel-sized clasts eroded from rocks of the poorly known Pacific Muck. We examine the systematic relationships of fossil fiddler crabs from Bahía Bique via synthetic and cladistic approaches, and conclude that they were from an extinct population of the extant <i>Uca ornata</i>. The fidelity of living–death assemblages between the Bique faunule and extant faunas of the tropical Eastern Pacific confirm the Quaternary age of the assemblage, and stimulate a detailed discussion of the preservation and palaeoecology of terrestrial and semi-terrestrial crabs in tropical assemblages.
DOI: 10.6084/m9.figshare.5346073
title: Clinical outcome in prostate cancer treated with magnetic resonance imaging-guided high-dose-rate brachytherapy combined with external beam radiotherapy

description: Clinical outcome in prostate cancer treated with magnetic resonance imaging-guided high-dose-rate brachytherapy combined with external beam radiotherapy
DOI: 10.6084/m9.figshare.5346091.v2
title: Hypoxia positron emission tomography imaging: combining information on perfusion and tracer retention to improve hypoxia specificity

description: <b>Background:</b> Static positron emission tomography (PET) allows mapping of tumor hypoxia, but low resolution and slow tracer retention/clearance results in poor image contrast and the risk of missing areas where hypoxic cells and necrosis are intermixed. Fully dynamic PET may improve accuracy but scan protocols suitable for routine clinical use are warranted. A modeling study proposed that hypoxia specificity can be improved by a clinically feasible blood-flow normalization procedure that only requires a 10- to 15-min dynamic scan (perfusion), followed by a short late static scan, but experimental validation is desired. <b>Methods:</b> Tumor-bearing mice were administered pimonidazole (hypoxia marker) and the PET hypoxia-tracer <sup>18</sup>F-azomycin arabinoside (FAZA) and scanned for 3h. Subsequently, the distributions of FAZA (autoradiography) and hypoxic cells (pimonidazole) were compared on tissue sections. PET images collected in 10-min time intervals between 60 and 90 min post-injection (PET<sub>early</sub>), which mimics the image contrast seen in patients, were compared voxel-by-voxel to 3-h PET (PET<sub>late</sub>). For comparison, PET<sub>early</sub> was normalized to the perfusion peak area, deduced from the first 10 min of the scan (PET<sub>perf</sub>), and the resulting parameter PET<sub>early</sub>/PET<sub>perf</sub> was compared with PET<sub>late</sub>. <b>Results:</b> Tissue analysis revealed a near-perfect spatial match between FAZA signal and hypoxic cell density (pimonidazole) 3 h post-injection, regardless of the tumor type. Only a weak inverse or no correlation between PET<sub>perf</sub> and PET<sub>late</sub> was seen, and the correlation between PET<sub>early</sub>/PET<sub>perf</sub> and PET<sub>late</sub> proved inferior to the correlation between PET<sub>early</sub> and PET<sub>late</sub>. <b>Conclusions:</b> Late PET scans in rodents, unlike patients, provide an accurate map of hypoxia against which earlier time-point scans can be compared. PET<sub>early</sub> and PET<sub>late</sub> correlated to a variable extent but the correlation was lowered by normalization to perfusion (PET<sub>early</sub>/PET<sub>perf</sub>). Our study challenges the validity/robustness of a perfusion normalization approach. This may reflect that the chaotic tumor vasculature uncouples microregional blood flow and oxygen extraction.
DOI: 10.6084/m9.figshare.5346073.v1
title: Clinical outcome in prostate cancer treated with magnetic resonance imaging-guided high-dose-rate brachytherapy combined with external beam radiotherapy

description: Clinical outcome in prostate cancer treated with magnetic resonance imaging-guided high-dose-rate brachytherapy combined with external beam radiotherapy
DOI: 10.6084/m9.figshare.5346073.v3
title: Clinical outcome in prostate cancer treated with magnetic resonance imaging-guided high-dose-rate brachytherapy combined with external beam radiotherapy

description: Clinical outcome in prostate cancer treated with magnetic resonance imaging-guided high-dose-rate brachytherapy combined with external beam radiotherapy
DOI: 10.6084/m9.figshare.5346073.v2
title: Clinical outcome in prostate cancer treated with magnetic resonance imaging-guided high-dose-rate brachytherapy combined with external beam radiotherapy

description: Clinical outcome in prostate cancer treated with magnetic resonance imaging-guided high-dose-rate brachytherapy combined with external beam radiotherapy
DOI: 10.6084/m9.figshare.5346085.v3
title: Automatic treatment planning facilitates fast generation of high-quality treatment plans for esophageal cancer

description: <b>Background:</b> The quality of radiotherapy planning has improved substantially in the last decade with the introduction of intensity modulated radiotherapy. The purpose of this study was to analyze the plan quality and efficacy of automatically (AU) generated VMAT plans for inoperable esophageal cancer patients. <b>Material and Methods:</b> Thirty-two consecutive inoperable patients with esophageal cancer originally treated with manually (MA) generated volumetric modulated arc therapy (VMAT) plans were retrospectively replanned using an auto-planning engine. All plans were optimized with one full 6MV VMAT arc giving 60 Gy to the primary target and 50 Gy to the elective target. The planning techniques were blinded before clinical evaluation by three specialized oncologists. To supplement the clinical evaluation, the optimization time for the AU plan was recorded along with DVH parameters for all plans. <b>Results:</b> Upon clinical evaluation, the AU plan was preferred for 31/32 patients, and for one patient, there was no difference in the plans. In terms of DVH parameters, similar target coverage was obtained between the two planning methods. The mean dose for the spinal cord increased by 1.8 Gy using AU (<i>p</i> = .002), whereas the mean lung dose decreased by 1.9 Gy (<i>p</i> p = .001). The median optimization time for AU plans was 117 min. <b>Conclusions:</b> The AU plans were in general preferred and showed a lower mean dose to the lungs. The automation of the planning process generated esophageal cancer treatment plans quickly and with high quality.
DOI: 10.6084/m9.figshare.5345983
title: De Boer et al. DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proceedings of the Royal Society B. DOI: 10.1098/rspb.2017-1182. Electronic Supplementary Material (ESM) Table S3

description: Data for products that yielded more than 0.5 ng/µl of DNA. Reads per species for nrITS1, nrITS2 and merged per sample.
DOI: 10.6084/m9.figshare.5345983.v1
title: De Boer et al. DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proceedings of the Royal Society B. DOI: 10.1098/rspb.2017-1182. Electronic Supplementary Material (ESM) Table S3

description: Data for products that yielded more than 0.5 ng/µl of DNA. Reads per species for nrITS1, nrITS2 and merged per sample.
DOI: 10.6084/m9.figshare.5346088.v3
title: The potential of hyperpolarized <sup>13</sup>C magnetic resonance spectroscopy to monitor the effect of combretastatin based vascular disrupting agents

description: <b>Background:</b> Targeting tumor vasculature with vascular disrupting agents (VDAs) results in substantial cell death that precede tumor shrinkage. Here, we investigate the potential of hyperpolarized magnetic resonance spectroscopy (HPMRS) to monitor early metabolic changes associated with VDA treatment. <b>Methods:</b> Mice bearing C3H mammary carcinomas were treated with the VDAs combretastatin-A4-phosphate (CA4P) or the analog OXi4503, and HPMRS was performed following [1-<sup>13</sup>C]pyruvate administration. Similarly, treated mice were positron emission tomography (PET) scanned following administration of the glucose analog FDG. Finally, metabolic imaging parameters were compared to tumor regrowth delay and measures of vascular damage, derived from dynamic contrast-agent enhanced magnetic resonance imaging (DCE-MRI) and histology. <b>Results:</b> VDA-treatment impaired tumor perfusion (histology and DCE-MRI), reduced FDG uptake, increased necrosis, and slowed tumor growth. HPMRS, revealed that the [1-<sup>13</sup>C]pyruvate-to-[1-<sup>13</sup>C]lactate conversion remained unaltered, whereas [1-<sup>13</sup>C]lactate-to-[<sup>13</sup>C]bicarbonate (originating from respiratory CO<sub>2</sub>) ratios increased significantly following treatment. <b>Conclusions:</b> DCE-MRI and FDG-PET revealed loss of vessel functionality, impaired glucose delivery and reduced metabolic activity prior to cell death. [1-<sup>13</sup>C]lactate-to-[<sup>13</sup>C]bicarbonate ratios increased significantly during treatment, indicating a decline in respiratory activity driven by the onset of hypoxia. HPMRS is promising for early detection of metabolic stress inflicted by VDAs, which cannot easily be inferred based on blood flow measurements.
DOI: 10.6084/m9.figshare.5345977
title: De Boer et al. DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proceedings of the Royal Society B. DOI: 10.1098/rspb.2017-1182. Electronic Supplementary Material (ESM) Table S2

description: Data for products that yielded less than 0.5 ng/µl of DNA. Reads per species for nrITS1, nrITS2 and merged per sample.
DOI: 10.6084/m9.figshare.5345977.v1
title: De Boer et al. DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proceedings of the Royal Society B. DOI: 10.1098/rspb.2017-1182. Electronic Supplementary Material (ESM) Table S2

description: Data for products that yielded less than 0.5 ng/µl of DNA. Reads per species for nrITS1, nrITS2 and merged per sample.
DOI: 10.15129/be4b52e4-ccbe-452e-ba99-0ab42e4e4a7c
title: Data for: "A Strathclyde cluster model for gait kinematic measurement using functional methods"

description: We developed an algorithm to measure the joint centres using Strathclyde Cluster Markers placed on the pelvis, thigh, leg and foot. Functional calibration movements were recorded for each joint prior to recording participants walkiing at their comfortable walking speed on a treadmill. The algorithm has been validated by the Vicon motion system. The validation experimental data are available in this dataset.
DOI: 10.6084/m9.figshare.5345572
title: Surgical outcome evaluation of perforated gastric cancer: from the aspects of both acute care surgery and surgical oncology

description: <b>Background:</b> Perforated gastric cancer (PGC) is a rare condition of gastric cancer (GC). In this study, we sought to assess the outcome of PGC from the aspects of both acute care surgery and surgical oncology at a single institute, Chang Gung Memorial Hospital (CGMH). <b>Methods:</b> From 1997 to 2013, 6864 patients were diagnosed with GC and 2738 were diagnosed with gastroduodenal perforation at CGMH. In total, 29 patients with PGC were identified. Immediate surgical and long-term oncologic outcomes were evaluated after an appropriate matching process was performed. <b>Results:</b> The immediate surgical outcome of PGC, i.e., the hospital mortality rate within 30 d after surgery, did not significantly differ from that of non-cancer related gastroduodenal perforation. The long-term oncologic outcome, with matching by age, gender, year of surgery and AJCC 7th stage grouping, also did not significantly differ from that of GC without perforation. <b>Conclusions:</b> Aggressive surgical treatment, including an initial emergency procedure for containing peritonitis and radical surgery for GC, may benefit PGC patients in terms of both the immediate and oncologic outcomes.
DOI: 10.6084/m9.figshare.5345572.v1
title: Surgical outcome evaluation of perforated gastric cancer: from the aspects of both acute care surgery and surgical oncology

description: <b>Background:</b> Perforated gastric cancer (PGC) is a rare condition of gastric cancer (GC). In this study, we sought to assess the outcome of PGC from the aspects of both acute care surgery and surgical oncology at a single institute, Chang Gung Memorial Hospital (CGMH). <b>Methods:</b> From 1997 to 2013, 6864 patients were diagnosed with GC and 2738 were diagnosed with gastroduodenal perforation at CGMH. In total, 29 patients with PGC were identified. Immediate surgical and long-term oncologic outcomes were evaluated after an appropriate matching process was performed. <b>Results:</b> The immediate surgical outcome of PGC, i.e., the hospital mortality rate within 30 d after surgery, did not significantly differ from that of non-cancer related gastroduodenal perforation. The long-term oncologic outcome, with matching by age, gender, year of surgery and AJCC 7th stage grouping, also did not significantly differ from that of GC without perforation. <b>Conclusions:</b> Aggressive surgical treatment, including an initial emergency procedure for containing peritonitis and radical surgery for GC, may benefit PGC patients in terms of both the immediate and oncologic outcomes.
DOI: 10.6084/m9.figshare.5345563
title: Single-molecule long-read transcriptome dataset of halophyte Halogeton glomeratus

description: The predicted CDSs of isoforms in <i>Halogeton glomeratus </i> transcriptome.
DOI: 10.6084/m9.figshare.5345464
title: Single-molecule long-read transcriptome dataset of halophyte Halogeton glomeratus

description: All of the isoform sequences of <i>Halogeton glomeratus</i> by Pacific Biosciences Isoform sequencing (Iso-Seq) technology
DOI: 10.6084/m9.figshare.5345563.v1
title: Single-molecule long-read transcriptome dataset of halophyte Halogeton glomeratus

description: The predicted CDSs of isoforms in <i>Halogeton glomeratus </i> transcriptome.
DOI: 10.6084/m9.figshare.5345413
title: Alien fishes in Australia

description: Data, computer code, and supplemental results from: <br>García-Díaz, P., Kerezsy, A., Unmack, P.J., Lintermans, M., Beatty, S.J., Butler, G.L., Freeman, R., Hammer, M.P., Hardie, S., Kennard, M.J., Morgan, D.L., Pusey, B.J., Raadik, T.A., Thiem, J.D., Whiterod, N., Cassey, P. & Duncan, R.P. (2018). Transport pathways shape the biogeography of alien freshwater fishes. Diversity and Distributions, https://onlinelibrary.wiley.com/doi/abs/10.1111/ddi.12777<br>Date last modified:22/05/2018Date uploaded: 04/10/2017<br>Please refer to the README file for further information
DOI: 10.6084/m9.figshare.5345464.v1
title: Single-molecule long-read transcriptome dataset of halophyte Halogeton glomeratus

description: All of the isoform sequences of <i>Halogeton glomeratus</i> by Pacific Biosciences Isoform sequencing (Iso-Seq) technology
DOI: 10.6084/m9.figshare.5345413.v1
title: Alien fishes in Australia

description: Data, computer code, and supplemental results from: <br>García-Díaz, P., Kerezsy, A., Unmack, P.J., Lintermans, M., Beatty, S.J., Butler, G.L., Freeman, R., Hammer, M.P., Hardie, S., Kennard, M.J., Morgan, D.L., Pusey, B.J., Raadik, T.A., Thiem, J.D., Whiterod, N., Cassey, P. & Duncan, R.P. (2018). Transport pathways shape the biogeography of alien freshwater fishes. Diversity and Distributions, https://onlinelibrary.wiley.com/doi/abs/10.1111/ddi.12777<br>Date last modified:22/05/2018Date uploaded: 04/10/2017<br>Please refer to the README file for further information
DOI: 10.6084/m9.figshare.5345221
title: Raw data. Mechanisms of facilitation by intertidal macroalgae influence macroinvertebrate distribution across stress scenarios. DOI: 10.3354/meps12355.

description: Raw data for the analyses presented in the manuscript.
DOI: 10.6084/m9.figshare.5345230
title: Tree-Structured Clustering in Fixed Effects Models

description: Fixed effects models are very flexible because they do not make assumptions on the distribution of effects and can also be used if the heterogeneity component is correlated with explanatory variables. A disadvantage is the large number of effects that have to be estimated. A recursive partitioning (or tree based) method is proposed that identifies clusters of units that share the same effect. The approach reduces the number of parameters to be estimated and is useful in particular if one is interested in identifying clusters with the same effect on a response variable. It is shown that the method performs well and outperforms competitors like the finite mixture model in particular if the heterogeneity component is correlated with explanatory variables. In two applications the usefulness of the approach to identify clusters that share the same effect is illustrated. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5345152
title: MTF_Lam_weekof_2017_08_23

description: Five computer vision sensors, or "Scouts," have been installed in Lam Square, inside of Rush Rhees Library at the University of Rochester. The Scouts collect data on how people move through Lam Square and generate heat maps based on those movements. This dataset contains data collected between 2017-08-16 and 2017-08-23. The dataset includes: (1) three .png heat maps for Scouts UR1, UR3 and UR5; Scouts UR2 and UR4 were not able to collect data (2) .jpg files of the background images that Scouts are observing, (3) JSON files detailing information on each Scout, the individual interaction captured by each Scout, an a summary of events.
DOI: 10.6084/m9.figshare.5345152.v1
title: MTF_Lam_weekof_2017_08_23

description: Five computer vision sensors, or "Scouts," have been installed in Lam Square, inside of Rush Rhees Library at the University of Rochester. The Scouts collect data on how people move through Lam Square and generate heat maps based on those movements. This dataset contains data collected between 2017-08-16 and 2017-08-23. The dataset includes: (1) three .png heat maps for Scouts UR1, UR3 and UR5; Scouts UR2 and UR4 were not able to collect data (2) .jpg files of the background images that Scouts are observing, (3) JSON files detailing information on each Scout, the individual interaction captured by each Scout, an a summary of events.
DOI: 10.6084/m9.figshare.5345221.v1
title: Raw data. Mechanisms of facilitation by intertidal macroalgae influence macroinvertebrate distribution across stress scenarios. DOI: 10.3354/meps12355.

description: Raw data for the analyses presented in the manuscript.
DOI: 10.6084/m9.figshare.5345230.v2
title: Tree-Structured Clustering in Fixed Effects Models

description: Fixed effects models are very flexible because they do not make assumptions on the distribution of effects and can also be used if the heterogeneity component is correlated with explanatory variables. A disadvantage is the large number of effects that have to be estimated. A recursive partitioning (or tree based) method is proposed that identifies clusters of units that share the same effect. The approach reduces the number of parameters to be estimated and is useful in particular if one is interested in identifying clusters with the same effect on a response variable. It is shown that the method performs well and outperforms competitors like the finite mixture model in particular if the heterogeneity component is correlated with explanatory variables. In two applications the usefulness of the approach to identify clusters that share the same effect is illustrated. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5345092
title: Supplemental genotyping-by-sequencing data for crested wheatgrass

description: These eight files are supplementary files for the Data in Brief article: <br>Li et al. (2017) Genotyping-by-sequencing data of 272 crested wheatgrass (Agropyron cristatum) genotypes. Data in Brief. https://dx.doi.org/10.1016/j.dib.2017.09.030<br>
DOI: 10.6084/m9.figshare.5345092.v1
title: Supplemental genotyping-by-sequencing data for crested wheatgrass

description: These eight files are supplementary files for the Data in Brief article: <br>Li et al. (2017) Genotyping-by-sequencing data of 272 crested wheatgrass (Agropyron cristatum) genotypes. Data in Brief. https://dx.doi.org/10.1016/j.dib.2017.09.030<br>
DOI: 10.6084/m9.figshare.5345230.v1
title: Tree-Structured Clustering in Fixed Effects Models

description: Fixed effects models are very flexible because they do not make assumptions on the distribution of effects and can also be used if the heterogeneity component is correlated with explanatory variables. A disadvantage is the large number of effects that have to be estimated. A recursive partitioning (or tree based) method is proposed that identifies clusters of units that share the same effect. The approach reduces the number of parameters to be estimated and is useful in particular if one is interested in identifying clusters with the same effect on a response variable. It is shown that the method performs well and outperforms competitors like the finite mixture model in particular if the heterogeneity component is correlated with explanatory variables. In two applications the usefulness of the approach to identify clusters that share the same effect is illustrated.
DOI: 10.6084/m9.figshare.5341294
title: Optimized microhydrated Ca(II) clusters, at the MP2/6-311++G** level of theory

description: These are structures of Ca2+(H2O)n clusters, optimized at the MP2/6-311++G** level of theory.