cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34894/d1mdkl
title: Replication Data for: Transcriptomic-based clustering of human atherosclerotic plaques identifies subgroups with different underlying biology and clinical presentation

description: &lt;strong&gt;Background&lt;/strong&gt;&lt;/br&gt;
These data are used in &lt;a href="https://doi.org/10.1101/2021.11.25.21266855" target="_blank"&gt;this paper&lt;/a&gt; by Mokry &lt;em&gt;et al.&lt;/em&gt;&lt;/br&gt;&lt;/br&gt;
&lt;strong&gt;Abstract&lt;/strong&gt;&lt;/br&gt;
Histopathological studies have revealed key processes of atherosclerotic plaque thrombosis. However, the diversity and complexity of lesion types highlight the need for improved sub-phenotyping. Here we analyze the gene expression profiles of 654 advanced human carotid plaques. The unsupervised, transcriptome-driven clustering revealed five dominant plaque types. These plaque phenotypes were associated with clinical presentation and showed differences in cellular compositions. Validation in coronary segments showed that the molecular signature of these plaques was linked to coronary ischemia. One of the plaque types with the most severe clinical symptoms pointed to both inflammatory and fibrotic cell lineages. This highlighted plaque phenotype showed high expression of genes involved in active inflammatory processes, neutrophil degranulation, matrix turnover, and metabolism. Further, we did a preliminary analysis of potential circulating biomarkers that mark the different plaques phenotypes. In conclusion, the definition of the plaque at risk for a thrombotic event can be fine-tuned by in-depth transcriptomic-based phenotyping. These differential plaque phenotypes prove clinically relevant for both carotid and coronary artery plaques and point to distinct underlying biology of symptomatic lesions.&lt;/br&gt;
&lt;/br&gt;
&lt;strong&gt;Athero-Express Biobank Study&lt;/strong&gt;&lt;/br&gt;
The AE started in 2002 and now includes over 3,500 patients who underwent surgery to remove atherosclerotic plaques (endarterectomy) from one (or more) of their major arteries (majority carotids and femorals); this is further described &lt;a href="https://doi.org/10.34894/4IKE3T" target="_blank"&gt;here&lt;/a&gt;. The study design and staining protocols are described by &lt;a href="https://pubmed.ncbi.nlm.nih.gov/15678794/" target="_blank"&gt;Verhoeven &lt;em&gt;et al.&lt;/em&gt;&lt;/a&gt;.&lt;/br&gt;&lt;/br&gt;

A link to the public GitHub repository can be found here: &lt;a href="https://github.com/CirculatoryHealth/PlaqueCluster" target="_blank"&gt;https://github.com/CirculatoryHealth/PlaqueCluster&lt;/a&gt;.&lt;/br&gt;&lt;/br&gt;

&lt;b&gt;Important notice on availability of data&lt;/b&gt;&lt;/br&gt;
The data are sensitive since they involve personal information of patients. There are also restrictions on use by commercial parties, and on sharing openly based on (inter)national laws and regulations and the written informed consent. Therefore these data (and additional clinical data) are only available upon discussion and signing a Data Sharing Agreement (see Terms of Access) and within a specially designed UMC Utrecht provided environment.&lt;/br&gt;&lt;/br&gt;
DOI: 10.3535/gjs-bb4-wwd
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ywe-01r-296
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.34894/r4bubc
title: Alike, But Not Quite: Comparing the Generalization of Pain-Related Fear and Pain-Related Avoidance

description: Pain-related fear and −avoidance crucially contribute to pain chronification. People with chronic pain may adopt costly avoidance strategies above and beyond what is necessary, aligning with experimental findings of excessive fear generalization to safe movements in these populations. Furthermore, recent evidence suggests that, when avoidance is costly, it can dissociate from fear. Here, we investigated whether concurrently measured pain-related fear and costly avoidance generalization correspond in one task. We also explored whether healthy participants avoid excessively despite associated costs, and if avoidance would decrease as a function of dissimilarity from a painassociated movement. In a robotic arm-reaching task, participants could avoid a low-cost, pain-associated movement trajectory (T+), by choosing a high-cost non-painful movement trajectory (T-), at opposite ends of a movement plane. Subsequently, in the absence of pain, we introduced three movement trajectories (G1-3) between T+ and T-, and one movement trajectory on the side of Topposite to T+ (G4), linearly increasing in costs from T+ to G4. Avoidance was operationalized as maximal deviation from T+, and as trajectory choice. Fear learning was measured using self-reported painexpectancy, pain-related fear, and startle eye-blink electromyography. Self-reports generalized, both decreasing with increasing distance from T+. In contrast, all generalization trajectories were chosen equally, suggesting that avoidance-costs and previous pain balanced each other out. No effects emerged in the electromyography. These results add to a growing body of literature showing that (pain-related) avoidance, especially when costly, can dissociate from fear, calling for a better understanding of the factors motivating, and mitigating, disabling avoidance.
Perspective: This article presents a comparison of pain-related fear- and avoidance generalization, and an exploration of excessive avoidance in healthy participants. Our findings show that painrelated avoidance can dissociate from fear, especially when avoidance is costly, calling for a better understanding of the factors motivating and mitigating disabling avoidance.
DOI: 10.3535/1cg-amh-qr4
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hs6-trd-pvz
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xb6-fj5z
title: PAN-00026128 - Late Medieval/modern spoon C9

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00026128&lt;/p&gt;
description: Modified: 2019-10-04T09:52:38+02:00
DOI: 10.34894/yeirrd
title: When Do We Not Face Our Fears? Investigating the Boundary Conditions of Costly Pain-Related Avoidance Generalization

description: Excessive generalization of fear and avoidance are hallmark symptoms of chronic pain disability, yet research focusing on the mechanisms underlying generalization of avoidance specifically, is scarce. Two experiments investigated the boundary conditions of costly painrelated avoidance generalization in healthy participants who learned to avoid pain by performing increasingly effortful (in terms of deviation and force) arm-movements using a robot-arm (acquisition). During generalization, novel, but similar arm-movements, without pain, were tested. Experiment 1 (N = 64) aimed to facilitate generalization to these movements by reducing visual contextual changes between acquisition and generalization, whereas Experiment 2 (N = 70) aimed to prevent extinction by increasing pain uncertainty. Both experiments showed generalization of pain-expectancies and pain-related fear. However, Experiment 2 was the first and only to also demonstrate generalization of avoidance, ie, choosing the novel effortful armmovements in the absence of pain. These results suggest that uncertainty about the occurrence of pain may delay recovery, due to reduced disconfirmation of threat beliefs when exploring, resulting in persistent avoidance.
Perspective: This article demonstrates generalization of instrumentally acquired costly painrelated avoidance in healthy people under conditions of uncertainty. The results suggest that targeting pain-related uncertainty may be a useful tool for clinicians adopting a psychological approach to treating excessive pain-related avoidance in chronic pain.
DOI: 10.3535/qt7-w8f-s6z
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s7j-rb8-1k1
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.34894/t4tplj
title: An In Vitro Model System Based on Calcium- and Phosphate Ion-Induced hMSC Spheroid Mineralization

description: A challenge in regenerative medicine is recapitulating the complex three-dimensional microenvironment of native organ or tissue, such as bone. Recreating the three-dimensional microenvironment of bone in the culture dish would allow the study of musculoskeletal disorders and the creation generation of building blocks for bone regeneration. In this study, we propose the use of a microwell-based platform to create spheroidal aggregates of human mesenchymal stromal cells and apply ionic calcium and phosphate supplementation to achieve rapid mineralization. These mineralized spheroids promote an osteogenic gene signature in cells through the influence of the spheroids biophysical environment and inorganic signaling, and require less calcium or phosphate to achieve mineralization compared to a monolayer culture. In addition, we found that mineralized spheroids represent a physiological model suitable for small molecule perturbations and the study of extracellular vesicle calcification. Furthermore, we demonstrate that understanding the molecular pathways promoted by the biophysical environment of spheroids allows mimicking these pathways in traditional monolayer culture, enabling similar rapid mineralization events. In sum, this study demonstrates the generation and application of physiological mineralized cell systems for multiple regenerative medicine goals.
DOI: 10.3535/8jx-xvv-v02
title: Lasiocampidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l79-vz9-mc3
title: Allotinus leogoron Fruhstorfer, 1915

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xb6-fkfh
title: Archeologisch Inventariserend Veldonderzoek De Strijp - Parc Solaire

description: &lt;p&gt;Een aantal proefsleuven om te bepalen of er resten zijn van Romeinse bewoning en/of verkaveling. Daarnaast zijn er resten uit het Neolithicum en IJzertijd mogelijk. Op het terrein wordt een aantal huizen gebouwd en zal een aantal rioolsleuven worden gegraven. Er zijn geen sporen en relevante artefacten gevonden. Het is niet uit te sluiten dat de Neolithische nederzetting zich tot op het noordelijk deel van het onderzoeksterrein uitstrekt. Het is echter niet waarschijnlijk. Het gebied bevond zich in de tijd van de bewoning twee meter lager dan de nederzetting, in een tijd dat de zeespiegel snel steeg. Verder zijn er geen aanwijzingen (artefacten, houtskool of sporen) voor bewoning gevonden.&lt;/p&gt;
DOI: 10.34894/u1ytw8
title: The Many Facets of Metacognition: Comparing Multiple Measures of Metacognition in Healthy

description: Metacognition is important for successful goal-directed behavior. We need to monitor and evaluate our cognition so that we can adapt our behavior when necessary. Metacognition consists of two main elements: metacognitive knowledge and online awareness. Online awareness, in turn, also consists of two elements: anticipation of performance and error recognition. Research into the interplay between these elements is currently lacking. Therefore, the aim of the current study was to explore how these different elements are related to each other. Healthy participants filled out the Metacognitive Awareness Inventory with two subscales that serve as measures of metacognitive knowledge. Next, as measures of online awareness, they performed a memory task and an abstract reasoning task (that were adapted to include trial-by-trial confidence judgments), and made pro- and retrospective confidence judgments about their performance on these tasks. The 128 included participants show a large variability in scores on all the different metacognitive measures. Better knowledge of cognition was associated with better regulation of cognition (r(126)=.656, p&lt;.001). On the memory task, better metacognitive sensitivity was associated with worse anticipation of performance (r(126)=.261, p=.003) but better evaluation of performance (r(126)=-.247, p=.005). On the abstract reasoning task, better anticipation of performance was associated with better evaluation of performance (r(126)=.266, p=.002). The current study confirms that metacognition is a multidimensional concept consisting of different elements that are associated with, but not equivalent to, each other. This knowledge is important for improving goal-directed behavior, which can be disturbed after, for example, brain damage.
DOI: 10.34894/ybqvzn
title: Cellular uptake of chemically modified mRNA occurs via caveolae-mediated endocytosis, yielding high levels of protein expression in slow-dividing cells

description: Nucleic acids have clear clinical potential for gene therapy. Plasmid DNA (pDNA) was the first nucleic acid to be pursued as a therapeutic molecule. Recently, mRNA came into play as it offers improved safety and affordability. In this study, we investigated the uptake mechanisms and efficiencies of genetic material by cells. We focused on three main variables: (1) the nucleic acid (pDNA, or chemically modified mRNA); (2) the delivery vector (Lipofectamine™️3000 or 3DFect™️); and (3) three human primary cells (mesenchymal stem cells, dermal fibroblasts, and osteoblasts). In addition, transfections were studied in a 3D environment using electrospun scaffolds. Cellular internalization of the complexes was assessed by using chemical inhibitors of endocytic pathways. Correlative light and electron microscopy were also used for this purpose. While lipoplexes utilized several entry routes, uptake via caveolae served as the main route for gene delivery. pDNA yielded higher expression levels in fast-dividing fibroblasts, whereas, in slow-dividing osteoblasts, cmRNA was responsible for high protein production. In the case of mesenchymal stem cells, which presented an intermediate doubling time, the combination vector/nucleic acid seemed more relevant than the nucleic acid per se. In all cases, protein expression was higher when the cells were seeded on 3D scaffolds.
DOI: 10.3535/cfm-c2r-st8
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nxj-0xk-wrg
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s78-3xg-a89
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v65-8hr-ecl
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xb6-fqm9
title: Heerenveen, De Wielen
title: Steekproef 2006-09/15

description: &lt;p&gt;onderzoeksrapport&lt;/p&gt;
description: &lt;p&gt;Steekproef 2006-09/15&lt;/p&gt;
DOI: 10.34894/chw0hb
title: Replication Data for: Combining acoustic tracking and LiDAR to study bat flight behaviour in three-dimensional space

description: Replication data for the manuscript 'Combining acoustic tracking and LiDAR to study bat flight behaviour in three-dimensional space'. Data from acoustic localisation of bats and LiDAR vegetation scans at sites that are part of the 'Light on Nature' project.
DOI: 10.3535/qlh-h2w-ghm
title: Lasiocampidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.34894/ev8iv2
title: Dendrochronologisch onderzoek Stolpboerderij De Vriendschap Hobrederweg 14 Midden-Beemster (BAAC project 16.0221)

description: Dendrochronological report
DOI: 10.3535/n9j-pr0-tv5
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x5l-4va-8v2
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xb6-g58k
title: PAN-00073564 - military button, Napoleonic: number Kingdom of Holland

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00073564&lt;/p&gt;
description: Modified: 2020-06-18T11:43:39+02:00
DOI: 10.34894/8nqiua
title: 22.056 Breda - Emerakker

description: De afdeling ruimte en erfgoed van de gemeente Breda leverde een boomstamput aan voor dendrochronologisch onderzoek. De boomstamput – aangeduid als waterput 64 – is bij archeologisch onderzoek in 1995 aangetroffen ter plaatse de Emerakker, naast het huidige Rath Verleghstadion. De boomstamput maakte deel uit van Merovingische bewoningssporen die zijn aantroffen. Een nabijgelegen boomstamput (waterput 63) werd dendrochronologisch gedateerd tussen 682 en 690.
Ondanks de lange tijd die is verstreken tussen berging en onderzoek is de boomstamput is goede conditie. Er zijn voldoende jaarringen aanwezig en het spinthout is intact bewaard gebleven.
De boomstamput is gekapt in de herfst of winter van 696/97 na Chr.
DOI: 10.3535/87v-e6g-xlt
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.34894/chtvj5
title: Circuit Class Training program
title: A group training program for stroke survivors

description: This training program is developed within University Medical Center Groningen, Center for Rehabilitation, location Beatrixoord. The training is intended to be performed under supervision of a therapist (occupational or physiotherapy). The participants are working in pairs and perform the exercises alternating while the observer is counting the repetitions.
DOI: 10.34894/tfwl3b
title: 22.057 Breda- Ridderstraat 8

description: In opdracht van de gemeente Breda is een is een moerbalk uit de Ridderstraat 8 dendrochronologisch onderzocht. De moerbalk is aangetroffen bij een renovatie van het gebouw en de vraag is of deze dateert van kort na de stadsbrand van 1534.
Het monster bevat ruim voldoende jaarringen en een deel van het spinthout is bewaard gebleven. De laatste jaarring dateert in 1603 waarmee het kapjaar rond 1610 komt te liggen, ruim na de stadsbrand.
DOI: 10.3535/q54-p49-z37
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zps-0p9-r19
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xb6-gdqm
title: Hijkersmilde, Veldhuizenweg, Gemeente Midden-Drenthe (Dr.). Een Inventariserend Archeologisch Veldonderzoek.

description: &lt;p&gt;onderzoeksrapport&lt;/p&gt;
DOI: 10.34894/dos1br
title: 22.078 Naarden - Naardermeer 13-15

description: dendrochronologisch onderzoek van een boerderij aan Naardermeer 13-15 te Naarden
DOI: 10.3535/73j-shg-wpn
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sky-s75-bzq
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.34894/e1ta3x
title: Fertility preferences in China in the 21st century

description: These files provide the entire search process of the metadata and the data and code of the meta-analysis which is used to investigate the trends of fertility preferences in China in the 21st century.
DOI: 10.3535/yyr-2cn-jp4
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.sbzqr2
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clarias gariepinus (Burchell, 1822)",
 "Country is Cuba",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088537-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/dans-xb6-ggem
title: PAN-00004569 - early medieval disc brooch enamelled group B

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00004569&lt;/p&gt;
DOI: 10.34894/iautsi
title: Dendrochronologisch onderzoek Weert Kasteel Nijenborgh beschoeiing van de gracht (BAAC project 20.0376)

description: Dendrochronological report
DOI: 10.3535/jfb-z03-w8f
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/njw-078-rw9
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.34894/d5ysxa
title: Replication Data for: Plantar Intrinsic Foot Muscle Activation during Functional Exercises compared to Isolated Foot Exercises in Younger Adults.

description: The data consist of raw and filtered non-invasive electromyography (EMG) data of 4 foot muscles while foot exercises are performed by non-symptomatic younger adults. The data package also contains summary measures (i.e., mean EMG amplitude and EMG integrated over time) and the scripts used to obtain these variables. The main goal of this study was to compare muscle activation of plantar intrinsic foot muscles, by means of EMG parameters, between functional exercises and isolated foot exercises. The secondary goal was to determine the effect of variations of foot exercises on the activation of the plantar intrinsic foot muscles.
description: Matlab, R2020b
DOI: 10.3535/n19-tnn-696
title: Lasiocampidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y25-gfa-r3c
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xb6-gght
title: PAN-00015521 - monochrome glass bead barrel/spherical shaped (unspecified)

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00015521&lt;/p&gt;
description: Modified: 2021-04-19T08:01:40+02:00
DOI: 10.34894/habm7o
title: Attention towards pupil size in humans and bonobos (Pan paniscus)

description: This publication package contains the accepted manuscript, all materials (i.e. the stimuli), raw data, processed data and the scripts used for analysis to be used by researchers for review of our findings as well as possible future work.
DOI: 10.34894/kxyhzg
title: 22.052 Haarlem - Antoniestraat

description: Door Cambium Botany zijn 2 monsters van de opgraving aan de Anthoniestraat te Haarlem aangeleverd voor dendrochronologisch onderzoek. De monsters zijn afkomstig van een duig en bodemplank van een waterput. Verdere informatie over de context is niet verstrekt.
Hoewel de monsters voldoende jaarringen bevatten, laten de metingen geen goede resultaten met referentiemateriaal te vinden.
DOI: 10.3535/0fw-hvw-wkj
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.34894/0nz1ir
title: 22.058 Nijmegen - Waalbandijk slachthuisterrein

description: dendrochronologisch onderzoek van 2 Romeinse tonnen van zilverspar
DOI: 10.3535/n8g-2ce-enn
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-xb6-gjqu
title: PAN-00046815 - coin/coin-related, Jan I (1268-1294), dubbele esterlin

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00046815&lt;/p&gt;
description: Modified: 2020-07-03T10:16:14+02:00
DOI: 10.3535/2g1-v2c-9tv
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.