cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22348153
title: Supplementary Material for: Surgical Treatment of Hepatocellular Carcinoma with a Tumor Thrombus Invading the Right Atrium: A Case Report

description: Up to 3% of all HCC present with a tumor thrombus (TT) in the inferior vena cava (IVC) and right atrium (RA). Extensive growth of HCC into the IVC and the RA is associated with a particularly poor prognosis. This clinical condition is related to a high risk of sudden death due to pulmonary embolism or acute heart failure. Therefore, a technically challenging treatment undergoing hepatectomy and cavo-atrial thrombectomy is necessary. We report a 61-year-old man presenting with right subcostal pain, progressive weakness and periodic shortness of breath for 3 months. He was diagnosed with advanced HCC with a tumor thrombus (TT) extending from the right hepatic vein into the inferior vena cava (IVC) and right atrium (RA). A multidisciplinary meeting with cardiovascular and hepatobiliary surgeons, oncologists, cardiologists, anesthesiologists and radiologists was held to determine the best treatment approach. Initially, the patient underwent right hemihepatectomy. As follows, the cardiovascular stage using cardiopulmonary bypass was successfully performed, removing the TT from the RA and ICV. In the early postoperative period the patient remained stable and was discharged on the 8th postoperative day. A morphological examination revealed Grade 2/3 HCC, a clear cell variant with the microvascular and macrovascular invasion. Immunohistochemical staining was positive for HEP-1, CD10, whereas negative for S100. The morphological and immunohistochemical results corresponded to HCC. The treatment of such patients requires the cooperation of various specialties. Although, the approach of the surgery is extremely complex including specific technical support, as well as high perioperative risks, the result offers favorable clinical outcomes.
DOI: 10.6084/m9.figshare.22924001
title: Supplementary Material for: Documented adverse drug reactions and discontinuation of angiotensin converting enzyme inhibitors and angiotensin receptor blockers in chronic kidney disease

description: Background: Angiotensin converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARB) are frequently discontinued in patients with chronic kidney disease (CKD). Documented adverse drug reactions (ADRs) in medical records may provide insight into the reasons for treatment discontinuation. Methods: In this retrospective cohort of U.S. veterans from 2005 to 2019, we identified individuals with CKD and a current prescription for an ACEi or ARB (current user group) or a discontinued prescription within the preceding 5 years (discontinued group). Documented ADRs in structured datasets associated with an ACEi or ARB were categorized into 17 pre-specified groups. Logistic regression assessed associations of documented ADRs with treatment discontinuation. Results: There were 882,441 (73.0%) individuals in the current user group and 326,794 (27.0%) in the discontinued group. There were 26,434 documented ADRs, with at least one documented ADR in 7,520 (0.9%) current users and 9,569 (2.9%) of the discontinued group. ADR presence was associated with treatment discontinuation, aOR 4.16 (95% CI 4.03, 4.29). The most common documented ADRs were cough (37.3%), angioedema (14.2%), and allergic reaction (10.4%). ADRs related to angioedema (aOR 3.81, 95% CI 3.47, 4.17), hyperkalemia (aOR 2.03, 95% CI 1.84, 2.24), peripheral edema (aOR 1.53, 95% CI 1.33, 1.77), or acute kidney injury (aOR 1.32, 95% CI 1.15, 1.51) were associated with treatment discontinuation. Conclusions: ADRs leading to drug discontinuation were infrequently documented. ADR types were differentially associated with treatment discontinuation. An understanding of which ADRs lead to treatment discontinuation provides an opportunity to address them at a healthcare system level.
DOI: 10.6084/m9.figshare.23122349
title: Supplementary Material for: <i>Mycobacterium avium</i> Complex Infections: Detailed Phenotypic and Functional Immunological Work-Up Is Required despite Genetic Analyses

description: <b><i>Introduction:</i></b> Cervical scrofulous lymphadenitis due to <i>Mycobacterium avium</i> complex (MAC) in immunocompetent adults is a rare disease. The presence of MAC infections demands meticulous clinical evaluation of patients along with detailed phenotypic and functional evaluation of their immune system including next-generation sequencing (NGS) analyses of target genes. <b><i>Methods:</i></b> Exact clinical histories of the index patients both suffering from retromandibular/cervical scrofulous lymphadenitis were obtained along with phenotypic and functional immunological evaluations of leukocyte populations followed by targeted NGS-based sequencing of candidate genes. <b><i>Results:</i></b> Immunological investigations showed normal serum immunoglobulin and complement levels, but lymphopenia, which was caused by significantly reduced CD3<sup>+</sup>CD4<sup>+</sup>CD45RO<sup>+</sup> memory T-cell and CD19<sup>+</sup> B-cell numbers. Despite normal T-cell proliferation to a number of accessory cell-dependent and -independent stimuli, the PBMC of both patients elaborated clearly reduced levels of a number of cytokines, including IFN-γ, IL-10, IL-12p70, IL-1α, IL-1β, and TNF-α upon TCR-dependent T-cell stimulation with CD3-coated beads but also superantigens. The IFN-γ production deficiency was confirmed for CD3<sup>+</sup>CD4<sup>+</sup> helper and CD4<sup>+</sup>CD8<sup>+</sup> cytotoxic T cells on the single-cell level by multiparametric flow cytometry irrespective of whether PMA/ionomycin-stimulated whole blood cells or gradient-purified PBMC was analyzed. In the female patient L1, targeted NGS-based sequencing revealed a homozygous c.110T&gt;C mutation in the interferon-γ receptor type 1 (IFNGR1) leading to significantly reduced receptor expression on both CD14<sup>+</sup> monocytes and CD3<sup>+</sup> T cells. Patient S2 presented with normal IFNGR1 expression on CD14<sup>+</sup> monocytes but significantly reduced IFNGR1 expression on CD3<sup>+</sup> T cells, despite the absence of detectable homozygous mutations in the IFNGR1 itself or disease-related target genes. Exogenous addition of increasing doses of IFN-γ resulted in proper upregulation of high-affinity FcγRI (CD64) on monocytes from patient S2, whereas monocytes from patient L1 showed only partial induction of CD64 expression after incubation with high doses of IFN-γ. <b><i>Conclusion:</i></b> A detailed phenotypic and functional immunological examination is urgently required to determine the cause of a clinically relevant immunodeficiency, despite detailed genetic analyses.
DOI: 10.23729/43d37797-e8cf-4190-80f1-ff567ec62836
title: Unmanned aircraft system (UAS) snow depth mapping at the Pallas Atmosphere-Ecosystem Supersite

description: The dataset contains digital elevation models (DEMs), orthophotomosaics, and field measurements from the Pallas Atmosphere-Ecosystem Supersite collected during 2018-2019. The DEMs were generated with the Structure from Motion (SfM) algorithm from images collected with several UAS (DJI Phantom 4 RTK, DJI Phantom 4 Advanced, DJI Mavic Pro, eBee Plus RTK). The field measurements include ground control points (GCPs) and checkpoints (CPs) utilized in generation and validation of the DEMs, and snow depth measurements collected from a snowline consisting of 46 snow stakes.
DOI: 10.35003/v9afaz
title: Shapefiles for count areas at Giordano Bruno, Moore F, North Ray, and South Ray

description: These are the crater and area shapefiles for count areas at Giordano Bruno, Moore F, North Ray, and South Ray.
DOI: 10.48324/dandi.000207/0.220216.0323
title: Data for: Neurons detect cognitive boundaries to structure episodic memories in humans (Zheng et al., 2022, Nat Neuro in press)

description: This dataset contains human single-neuron data recorded from the medial temporal lobe (MTL) during a set of experiments to explore the role of neurons that respond to cognitive boundaries. This dataset accompanies the paper cited below. Example code on how to plot this data can be found at https://github.com/rutishauserlab/cogboundary-zheng .

Reference (to be updated upon publication):  Cognitive boundary signals in the human medial temporal lobe shape episodic memory representation. Jie Zheng, Andrea Gómez Palacio Schjetnan, Mar Yebra, Clayton Mosher, Suneil Kalia, Taufik A. Valiante, Adam N. Mamelak, Gabriel Kreiman, Ueli Rutishauser. bioRxiv 2021.01.16.426538.  [Nat Neuro, in press, 2022]
DOI: 10.5066/p9mjhtmq
title: Predicted 2020 densities for 11 songbird species across the western United States

description: Informed wildlife management requires robust information regarding population status, habitat requirements, and likely responses to changing resource conditions. Growing evidence indicates single species management may inadequately conserve communities and result in undesired effects to non-target species. Thus, management can benefit from habitat relationship information for multiple species within, and across, ecosystems. Using 13 years of point count data (2008-2020) collected across the western United States and a suite of relevant covariates for habitat, we fit hierarchical models to characterize and predict songbird densities and evaluate population trends for 11 species of interest: Bewick’s Wren (Thryomanes bewickii; BEWR), Brewer’s Sparrow (Spizella breweri; BRSP), Black-throated Gray Warblers (Setophaga nigrescens; BTYW), Gray Flycatcher (Empidonax wrightii; GRFL), Gray Vireo (Vireo vicinior; GRVI), Green-tailed Towhee (Pipilo chlorurus; GTTO), Juniper Titmouse (Baeolophus ridgwayi; JUTI), Loggerhead Shrike (Lanius ludovicianus; LOSH), Sagebrush Sparrow (Amphispiza belli; SABS), Sage Thrasher (Oreoscoptes montanus; SATH), and Townsend’s Solitaire (Myadestes townsendi; TOSO). The resulting maps include density (birds/km2) for each species (BEWR_2020_PredictedDensity.tif, BRSP_2020_PredictedDensity.tif, BTYW_2020_PredictedDensity.tif, GRFL_2020_PredictedDensity.tif, GRVI_2020_PredictedDensity.tif, GTTO_2020_PredictedDensity.tif, JUTI_2020_PredictedDensity.tif, LOSH_2020_PredictedDensity.tif, SABS_2020_PredictedDensity.tif, SATH_2020_PredictedDensity.tif, and TOSO_2020_PredictedDensity.tif), given 2020 environmental conditions, as well as masks representing all raster cells where one or more covariate pixel value(s) fell outside of the 2.5 and 97.5 percent quantiles of the covariate sample used when fitting the model (BEWR_mask_raster_2020.tif, BRSP_mask_raster_2020.tif, BTYW_mask_raster_2020.tif, GRFL_mask_raster_2020.tif, GRVI_mask_raster_2020.tif, GTTO_mask_raster_2020.tif, JUTI_mask_raster_2020.tif, LOSH_mask_raster_2020.tif, SABS_mask_raster_2020.tif, SATH_mask_raster_2020.tif, and TOSO_mask_raster_2020.tif). Values of one within the mask layers indicate there may be considerable uncertainty associated with the predicted values and/or that values may be unusually high or low.
DOI: 10.5066/p9qftk1d
title: Prioritized sites for conifer removal within the Utah portion of Bird Conservation Region 16, 2020

description: Individual species often drive habitat restoration action; however, management under this paradigm may negatively affect non-target species. Prioritization frameworks which explicitly consider benefits to target species while minimizing consequences for non-target species may drastically improve management strategies. We examined extents to which conifer removal, an approach frequently implemented to restore sagebrush ecosystems, can be conducted without detrimental effects to conifer-associated species, including the imperiled Pinyon Jay (Gymnorhinus cyanocephalus). Additionally, we predicted abundance responses for multiple species following simulated conifer removal at sites selected to achieve variable management objectives. We used model-predicted changes in species’ densities following simulated conifer removal to identify optimal removal sites under single species, multi-species (ecosystem), and multi-ecosystem management scenarios. We simulated conifer removal at prioritized sites under these scenarios using an integer linear programming algorithm and evaluated resulting abundances for six songbird species. The resulting maps represent prioritized pixels for conifer removal inside of priority areas for conservation (PACs) which occur within the Utah portion of Bird Conservation Region 16. Sites identified to receive conifer removal treatments which minimize effects to the pinyon jay, under three different budget scenarios, are represented in three raster layers: pija_3.tif, pija_6.tif, pija_9.tif. Sites identified for conifer removal treatments which maximize outcomes for Brewer’s Sparrow are represented in brsp_6.tif. Sites identified for conifer removal treatments which maximize outcomes for sagebrush-associated species; Brewer’s Sparrow (Spizella breweri), Sagebrush Sparrow (Artemisiospiza nevadensis), and Sage Thrasher (Oreoscoptes montanus) are represented in sb_ecosystem_6.tif. Sites identified for conifer removal which minimize negative outcomes for pinyon-juniper associated species; Bewick’s Wren (Thryomanes bewickii), Gray Flycatcher (Empidonax wrightii), and Pinyon Jay are represented in pj_ecosystem_6.tif. Sites identified for conifer removal treatments which maximize outcomes for all six songbird species are represented in multi_ecosystem_6.tif. Sites identified for conifer removal treatments which maximize outcomes for Brewer’s Sparrow, Sagebrush Sparrow, and Sage Thrasher and which weight outcomes for Pinyon Jay three times more heavily than the other species are represented in sb_ecoystem_pijawt_6.tif. Finally, sites identified for conifer removal treatments which maximize outcomes for all six species, while weighting outcomes for Pinyon Jay three times more heavily than all other species are represented in multi_ecoystem_pijawt_6.tif.
DOI: 10.6084/m9.figshare.23628591
title: Supplementary Material for: Tortuosity and Proximal-Specific Hemodynamics Associated with Plaque Location in the Carotid Bulb Stenosis

description: Background: The occurrence of carotid bulb plaque is a complex process. We aimed to investigate plaque characteristics and geometric and hemodynamic parameters among patients with body and apical plaques of the carotid bulb and to identify the mechanism of bulb plaque formation and location. Methods: Consecutive patients with single carotid bulb stenosis (50–99%) were enrolled retrospectively. Patients were divided into body and apical plaque groups based on plaque location. Plaque location and characteristics were identified and measured on high-resolution vessel wall magnetic resonance imaging. Geometric parameters were derived from time-of-flight magnetic resonance imaging. Computational fluid dynamics simulations were performed to quantify wall shear stress (WSS). Results: Seventy patients were recruited (41 body plaques and 29 apical plaques). WSSplaque values were lower than WSSnon-plaque values for all plaques (median [IQR], 12.59 [9.83-22.14] vs. 17.27 [11.63-27.63] Pa, p = 0.001). In a multivariate binary logistic regression, the tortuosity of the stenosed region, the magnitudes of the mean relative residence time, and the minimum transverse WSS in the proximal part of the lesion were the key factors independently associated with plaque location (p = 0.022, 0.013, and 0.012, respectively). Conclusions: Plaque formation was associated with local flow pattern, and the tortuosity and proximal-specific hemodynamics were significantly associated with plaque location in the carotid bulb.
DOI: 10.6084/m9.figshare.24155487
title: Supplementary Material for: Documented Reperfusion of the Retina on Fluorescein Angiography after Administration of Intravenous Prostaglandin E1 for Central Retinal Artery Occlusion: A Case Report

description: Central retinal artery occlusion (CRAO) can result in devastating permanent vision loss. Presently, there is no evidence-based treatment for CRAO that is widely accepted. In the literature, multiple studies propose intravenous prostaglandin E1 (IV PGE1) as a potential treatment option for patients with CRAO. We illustrate two cases of CRAO successfully treated with IV PGE1. In both cases, our patients with vascular risk factors were diagnosed with CRAO of the left eye. They were started on twice daily intravenous (IV) 40 mcg PGE1 in 100 mL normal saline, with each dose administered over three hours. In the first case, we documented reperfusion of the retina on fluorescein angiography after administration of IV PGE1. In the second case, our patient improved from no light perception (NLP) visual acuity (VA) to count fingers (CF) VA within 48 hours of treatment with IV PGE1. Our study highlights the vasodilatory effect of IV PGE1. Due to its mechanism of action and safety profile, it should be considered a potential treatment option for CRAO. Further randomized controlled trials are necessary to determine the overall therapeutic effect of IV PGE1 for CRAO.
DOI: 10.7302/xx1r-zg70
title: .stl file of Circle of Willis

description: This .stl file represents the largest vessels of the cerebral circulation, specifically around the Circle of Willis. The file was created from a Computed Tomography Angiography (CTA) of a relatively healthy patient. It consisted of a 512 x 512 x 709 voxel image with a resolution of 0:35 mm x 0:35 mm x 0:5 mm.
The model includes the basilar artery (1), left and right internal carotid arteries (2, and 3), left and right anterior cerebral arteries (4, and 5), left and right middle cerebral arteries (6, and 7), left and right posterior cerebral arteries (8, and 9), and various communicating arteries (10, 11, and 12).
description: The .stl file of the main arteries in the Circle of Willis was created from Computed Tomography Angiography (CTA) data using a segmentation procedure whereby the arterial lumen boundary was defined using a combination of manual demarcation, image thresholding, and level-set segmentation [1,2]. A set of vessel centerline paths and 2-D segmentations along each path were produced
description: from these a 3-D geometric solid model defined by non-uniform rational B-splines (NURBS) was created.
description: [1] N. Wilson, K. Wang, R. Dutton, C.A. Taylor, "A software framework for creating patient specific geometric models from medical imaging data for simulation based medical planning of vascular surgery", Medical Image Computing and Computer-Assisted Intervention MICCAI 2001, Springer, 2001, pp. 449–456. doi: 10.1007/3-540-45468-3_54
[2] N. Xiao, J.D. Humphrey, C.A. Figueroa, "Multi-Scale Computational Model of Three-Dimensional Hemodynamics within a Deformable Full-Body Arterial Network”, Journal of Computational Physics, 2013, Vol 244, pp. 22-40. doi: 10.1016/j.jcp.2012.09.016
DOI: 10.5066/p9nig4uw
title: Predicted Pinyon Jay (Gymnorhinus cyanocephalus) densities across the western United States, 2008-2020

description: Management intended to benefit a target species may also affect non-target species that co-occur over space and time. Pinyon jay (Gymnorhinus cyanocephalus) populations experienced long-term declines and rely on habitat that could be lost to conifer removal programs for greater sage-grouse (Centrocercus urophasianus). Using 13 years of point count data (2008-2020) collected across the western United States and a suite of relevant covariates for habitat, we fit a hierarchical model to characterize and predict pinyon jay densities and evaluate population trends. The resulting maps include pinyon jay density at the beginning (PIJA_2008_PredictedDensity.tif) and end (PIJA_2020_PredictedDensity.tif) of our study period, a map depicting the percent change (difference) between the two years (PIJA_MedianDensityChange_2008to2020.tif), as well as masks representing all raster cells where one or more covariate pixel value(s) fell outside of the 2.5 and 97.5 percent quantiles of the covariate sample used when fitting the model, which could result in unusually high or low predictions of pinyon jay density (PIJA_mask_raster_2008.tif and PIJA_mask_raster_2020.tif).
DOI: 10.5281/zenodo.8362384
title: Stochastic Turing patterns of trichomes in Arabidopsis leaves. Data and Software.

description: Data and Software.
DOI: 10.5287/bodleian:mzj7ywxvo
title: STN local field potential recordings from awake patients with Parkinson’s, ON and OFF meds, and during 130 Hz DBS
DOI: 10.5287/bodleian:rj7jyjx97
title: Analysis code for publication: 'The aperiodic exponent of subthalamic field potentials reflects excitation/inhibition balance in Parkinsonism'
DOI: 10.5287/bodleian:wx6d7oenk
title: Wideband recordings from silicon probes in the subthalamic nucleus of 6-OHDA hemi-lesioned rats during anaesthesia
DOI: 10.6080/k0g15xs1
title: Extracellular recordings from multi-site silicon probes in the anterior thalamus and subicular formation of freely moving mice.
title: CRCNS.org th-1

description: The data set contains recordings made from multiple anterior thalamic nuclei, mainly the antero-dorsal (AD) nucleus, and subicular areas, mainly the post-subiculum (PoS), in freely moving mice. Thalamic and subicular electrodes yielding high number of the so-called Head-Direction (HD) cells were likely to be located in the AD nucleus and the PoS, respectively. Electrode placement was confirmed by histology. The data was obtained during 42 recording sessions and includes responses of 720 neurons in the thalamus and 357 neurons in the PoS, in seven animals while they foraged for food in an open environment (53- x 46-cm).
DOI: 10.6084/m9.figshare.23584020
title: Supplementary Material for: Effectiveness of water-assisted colonoscopy without sedation in patients with ulcerative colitis

description: Introduction Studies have found that water-assisted colonoscopy (WAC) including water immersion colonoscopy (WIC) and water exchange colonoscopy (WEC) is superior to air insufflation colonoscopy (AIC) in terms of the cecal intubation rate. However, the application of WAC in ulcerative colitis (UC) has rarely been reported. This study aims to explore the effectiveness of WAC without sedation in patients with UC. Methods 172 UC patients were randomly divided into the AIC group (n=56), WIC group (n=58) and WEC group (n=58). The cecal intubation rate, abdominal pain score, operator difficulty, bowel cleanliness, insertion and total time were compared. Results The cecal intubation rate was higher in the WIC (91.4% vs. 75.0%; mean difference=16.4%, 95%CI 3.0%-29.8%) and WEC (93.1% vs. 75.0%; mean difference=18.1%, 95%CI 5.0%-31.2%) compared to the AIC group, while there was no difference between the WIC and WEC groups. The abdominal pain score and operator difficulty were lower in the WIC and WEC groups than in the AIC group, while there was no difference between the WIC and WEC groups. The bowel cleanliness during withdrawal was higher in the WIC and WEC groups than in the AIC group, while the WEC was superior to WIC. Compared with the AIC and WIC groups, the insertion time and total time were longer in the WEC group, and there was no difference in the AIC group and WIC group. Conclusion In comparison with AIC, WAC can increase the cecal intubation rate, reduce abdominal pain scores and improve bowel cleanliness in patients with UC.
DOI: 10.6084/m9.figshare.24448891
title: Data of tuberculosis and climate in the Kendari district, indonesia

description: Data on Tuberculosis and climate in the Kendari district, Indonesia
DOI: 10.6084/m9.figshare.24448891.v1
title: Data of tuberculosis and climate in the Kendari district, indonesia

description: Data on Tuberculosis and climate in the Kendari district, Indonesia
DOI: 10.5519/qd.i9klntzn
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (5342804 records)
DOI: 10.17632/n9v2jhhkc4.2
title: DMT310-003 - Supplemental Figure 1

description: Spicule of Spongilla lacustris (200x magnification)
DOI: 10.17632/n9v2jhhkc4.1
title: DMT310-003 - Supplemental Figure 1

description: Spicule of Spongilla lacustris (200x magnification)
DOI: 10.17632/pkpxmkv3ys.2
title: DMT310-003 Supplemental Table 1

description: List of exclusionary treatments and their washout period