cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7544194
title: Mouse Organoids imaged with Dual Oblique Plane Microscopy

description: This is a dataset to demonstrate segmenting colonies of 3D cells. The primary focus is segmenting mouse organoids images using timelapse dual oblique plane microscopy. There is also a set of data mouse embryonic stem cells imaged using spinning disk confocal microscopy.
DOI: 10.5281/zenodo.7544193
title: Mouse Organoids imaged with Dual Oblique Plane Microscopy

description: This is a dataset to demonstrate segmenting colonies of 3D cells. The primary focus is segmenting mouse organoids images using timelapse dual oblique plane microscopy. There is also a set of data mouse embryonic stem cells imaged using spinning disk confocal microscopy.
DOI: 10.5281/zenodo.7520182
title: Familiar object benefit more from transsaccadic feature predictions

description: The transsaccadic feature prediction mechanism associates peripheral and foveal information<br> belonging to the same object to make predictions about how an object seen in the periphery<br> would appear in the fovea or vice versa. It is unclear if such transsaccadic predictions require<br> experience with the object such that only familiar objects benefit from this mechanism by virtue<br> of having peripheral-foveal associations. In two experiments, we tested whether familiar<br> objects have an advantage over novel objects in peripheral-foveal matching and transsaccadic<br> change detection tasks.<br> In both experiments, observers were unknowingly familiarized with a small set of stimuli by<br> completing a sham orientation change detection task. In the first experiment, observers<br> subsequently performed a peripheral-foveal matching task, where they needed to pick the<br> foveal test object that matched a briefly presented peripheral target. In the second experiment,<br> observers subsequently performed a transsaccadic object change detection task where a<br> peripheral target was exchanged or not exchanged with another target after the saccade, either<br> immediately or after a 300 ms blank period.<br> We found an advantage of familiar objects over novel objects in both experiments. While<br> foveal-peripheral associations explained the familiarity effect in the matching task of the first<br> experiment, the second experiment provided evidence for the advantage of peripheral-foveal<br> associations in transsaccadic object change detection. Introducing a postsaccadic blank<br> improved the change detection performance in general but more for familiar than for novel<br> objects. We conclude that familiar objects benefit from additional object-specific predictions.<br> Keywords: Saccades, Transsaccadic prediction, perceptual learning, object recognition,<br> visual stability.
DOI: 10.5281/zenodo.7520181
title: Familiar object benefit more from transsaccadic feature predictions

description: The transsaccadic feature prediction mechanism associates peripheral and foveal information<br> belonging to the same object to make predictions about how an object seen in the periphery<br> would appear in the fovea or vice versa. It is unclear if such transsaccadic predictions require<br> experience with the object such that only familiar objects benefit from this mechanism by virtue<br> of having peripheral-foveal associations. In two experiments, we tested whether familiar<br> objects have an advantage over novel objects in peripheral-foveal matching and transsaccadic<br> change detection tasks.<br> In both experiments, observers were unknowingly familiarized with a small set of stimuli by<br> completing a sham orientation change detection task. In the first experiment, observers<br> subsequently performed a peripheral-foveal matching task, where they needed to pick the<br> foveal test object that matched a briefly presented peripheral target. In the second experiment,<br> observers subsequently performed a transsaccadic object change detection task where a<br> peripheral target was exchanged or not exchanged with another target after the saccade, either<br> immediately or after a 300 ms blank period.<br> We found an advantage of familiar objects over novel objects in both experiments. While<br> foveal-peripheral associations explained the familiarity effect in the matching task of the first<br> experiment, the second experiment provided evidence for the advantage of peripheral-foveal<br> associations in transsaccadic object change detection. Introducing a postsaccadic blank<br> improved the change detection performance in general but more for familiar than for novel<br> objects. We conclude that familiar objects benefit from additional object-specific predictions.<br> Keywords: Saccades, Transsaccadic prediction, perceptual learning, object recognition,<br> visual stability.
DOI: 10.5281/zenodo.7544223
title: Expression Profile of CD157 Reveals Functional Heterogeneity of Capillaries in Human Dermal Skin

description: CD157 acts as a receptor, regulating leukocyte trafficking and the binding of extracellular matrix components. However, the expression pattern and the role of CD157 in human blood (BEC) and the lymphatic endothelial cells (LEC) of human dermal microvascular cells (HDMEC), remain elusive. We demonstrated constitutive expression of CD157 on BEC and LEC, in fetal and juvenile/adult skin, in situ, as well as in isolated HDMEC. Interestingly, CD157 epitopes were mostly localized on BEC, co-expressing high levels of CD31 (CD31<sup>High</sup>), as compared to CD31<sup>Low</sup> BEC, whereas the podoplanin expression level on LEC did not affect CD157. Cultured HDMEC exhibited significantly higher numbers of CD157-positive LEC, as compared to BEC. Interestingly, separated CD157<sup>-</sup> and CD157<sup>+</sup> HDMEC demonstrated no significant differences in clonal expansion in vitro, but they showed distinct expression levels of cell adhesion molecules, before and after cytokine stimulation in vitro. In particular, we proved the enhanced and specific adherence of CD11b-expressing human blood myeloid cells to CD157<sup>+</sup> HDMEC fraction, using an in vitro immune-binding assay. Indeed, CD157 was also involved in chemotaxis and adhesion of CD11b/c monocytes/neutrophils in prevascularized dermo-epidermal skin substitutes (vascDESS) in vivo. Thus, our data attribute specific roles to endothelial CD157, in the regulation of innate immunity during inflammation.
DOI: 10.5281/zenodo.7544222
title: Expression Profile of CD157 Reveals Functional Heterogeneity of Capillaries in Human Dermal Skin

description: CD157 acts as a receptor, regulating leukocyte trafficking and the binding of extracellular matrix components. However, the expression pattern and the role of CD157 in human blood (BEC) and the lymphatic endothelial cells (LEC) of human dermal microvascular cells (HDMEC), remain elusive. We demonstrated constitutive expression of CD157 on BEC and LEC, in fetal and juvenile/adult skin, in situ, as well as in isolated HDMEC. Interestingly, CD157 epitopes were mostly localized on BEC, co-expressing high levels of CD31 (CD31<sup>High</sup>), as compared to CD31<sup>Low</sup> BEC, whereas the podoplanin expression level on LEC did not affect CD157. Cultured HDMEC exhibited significantly higher numbers of CD157-positive LEC, as compared to BEC. Interestingly, separated CD157<sup>-</sup> and CD157<sup>+</sup> HDMEC demonstrated no significant differences in clonal expansion in vitro, but they showed distinct expression levels of cell adhesion molecules, before and after cytokine stimulation in vitro. In particular, we proved the enhanced and specific adherence of CD11b-expressing human blood myeloid cells to CD157<sup>+</sup> HDMEC fraction, using an in vitro immune-binding assay. Indeed, CD157 was also involved in chemotaxis and adhesion of CD11b/c monocytes/neutrophils in prevascularized dermo-epidermal skin substitutes (vascDESS) in vivo. Thus, our data attribute specific roles to endothelial CD157, in the regulation of innate immunity during inflammation.
DOI: 10.35078/jk1340
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Teófilo Otoni| Município: Senhora do Porto

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.6084/m9.figshare.19834356
title: Field assessment of trace element phytoextraction by different <i>Populus</i> clones established on brownfields in southern Quebec (Canada)

description: Fast-growing hybrid poplars have been tested for their potential to remove trace elements (TE) from polluted soil in several temperate regions. Despite their potential, they have rarely been tested in countries with a cold temperate climate. The current study screened four different <i>Populus</i> hybrids for phytoextraction of four TEs (i.e., As, Cu, Pb, and Zn) on an abandoned brownfield site in southern Quebec (Canada). The main results showed that under the current experimental conditions, the most important traits determining the actual phytoextraction rate are Biological Concentration Factor (BCF) and TE accumulation in the aboveground biomass, rather than biomass productivity. Although the overall performance of the chosen hybrids was rather poor, the presence of poplar stands enhanced the movement of mobile contaminants in soil, which led to an increase in their concentration in the root zone. This aspect suggests possible strategies for using these plants with high transpiration rates in future phytoremediation projects, including either possible rotation with more effective TE phytoextractor plants (e.g., hyperaccumulators) that can remove high TE amounts that have migrated from the deeper soil layers following poplar plantation, or phytostabilization. Although the use of fast-growing woody species is commonly reported as a feasible option for the phytoextraction of TEs in temperate climates, most available information pertains to only a few species, mostly willows. This is one of the few studies reporting the results of a field test carried out in a cold temperate region, in which different poplar hybrid clones were tested for their potential in TEs phytoextraction. This research determined that although the studied poplar genotypes have no potential under these experimental conditions, the increase in TE concentration observed in the rhizosphere after two years suggests possible alternative phytoremediation strategies (phytostabilization) for managing polluted sites in cold temperate climates.
DOI: 10.6084/m9.figshare.19834356.v1
title: Field assessment of trace element phytoextraction by different <i>Populus</i> clones established on brownfields in southern Quebec (Canada)

description: Fast-growing hybrid poplars have been tested for their potential to remove trace elements (TE) from polluted soil in several temperate regions. Despite their potential, they have rarely been tested in countries with a cold temperate climate. The current study screened four different <i>Populus</i> hybrids for phytoextraction of four TEs (i.e., As, Cu, Pb, and Zn) on an abandoned brownfield site in southern Quebec (Canada). The main results showed that under the current experimental conditions, the most important traits determining the actual phytoextraction rate are Biological Concentration Factor (BCF) and TE accumulation in the aboveground biomass, rather than biomass productivity. Although the overall performance of the chosen hybrids was rather poor, the presence of poplar stands enhanced the movement of mobile contaminants in soil, which led to an increase in their concentration in the root zone. This aspect suggests possible strategies for using these plants with high transpiration rates in future phytoremediation projects, including either possible rotation with more effective TE phytoextractor plants (e.g., hyperaccumulators) that can remove high TE amounts that have migrated from the deeper soil layers following poplar plantation, or phytostabilization. Although the use of fast-growing woody species is commonly reported as a feasible option for the phytoextraction of TEs in temperate climates, most available information pertains to only a few species, mostly willows. This is one of the few studies reporting the results of a field test carried out in a cold temperate region, in which different poplar hybrid clones were tested for their potential in TEs phytoextraction. This research determined that although the studied poplar genotypes have no potential under these experimental conditions, the increase in TE concentration observed in the rhizosphere after two years suggests possible alternative phytoremediation strategies (phytostabilization) for managing polluted sites in cold temperate climates.
DOI: 10.6084/m9.figshare.21746098
title: Understanding quality data correctly: a randomized comparison of presentation formats among cancer patients and relatives

description: <b>Background:</b> Patient representatives are increasingly engaged in quality in health care, and even though quality data are publicly available, correct interpretation may be challenging. We designed a randomized study with the primary aim to examine the association between preferred data presentation format and the interpretation of quality data among cancer patients and relatives. <b>Material and methods:</b> Surveys were distributed to the Danish Cancer Society Citizens’ Panel between 31 March and 14 April 2019 and 55% completed the survey (<i>N</i> = 464) including six storyboards that presented authentic quality data in table format, league table and point estimates. The storyboards were randomized to expose participants to the data in the three different formats and in varying presentation order. Logistic regression models were used to calculate Odds Ratios (ORs) and 95% confidence intervals (CIs) for the association between preferred presentation format, health literacy, education and cohabitation status as exposures and interpretation of quality data as outcome. <b>Results:</b> The majority of participants (97%) had high literacy and 57% had a medium or long higher education. A total of 60% found the questions difficult or very difficult and 33% were not able to correctly interpret at least one format. Correct interpretation was associated with preferred league table (OR = 1.62; 95% CI = 1.04–5.52) and if the data was presented in the preferred format. Medium and long education were associated with correct interpretation of at least one format (OR = 1.93; 95% CI = 1.16–3.21 and OR = 3.89; 95% CI = 1.90–7.95, respectively) while health literacy and cohabitation status were not. <b>Conclusions:</b> More than one third of the participants were not able to correctly interpret the data and the understanding of quality data improved with longer education and if the data was presented in the preferred format. Decision-makers should carefully consider displaying quality data according to preferred presentation format and to guide interpretation for individuals with short education.
DOI: 10.6084/m9.figshare.21746098.v1
title: Understanding quality data correctly: a randomized comparison of presentation formats among cancer patients and relatives

description: <b>Background:</b> Patient representatives are increasingly engaged in quality in health care, and even though quality data are publicly available, correct interpretation may be challenging. We designed a randomized study with the primary aim to examine the association between preferred data presentation format and the interpretation of quality data among cancer patients and relatives. <b>Material and methods:</b> Surveys were distributed to the Danish Cancer Society Citizens’ Panel between 31 March and 14 April 2019 and 55% completed the survey (<i>N</i> = 464) including six storyboards that presented authentic quality data in table format, league table and point estimates. The storyboards were randomized to expose participants to the data in the three different formats and in varying presentation order. Logistic regression models were used to calculate Odds Ratios (ORs) and 95% confidence intervals (CIs) for the association between preferred presentation format, health literacy, education and cohabitation status as exposures and interpretation of quality data as outcome. <b>Results:</b> The majority of participants (97%) had high literacy and 57% had a medium or long higher education. A total of 60% found the questions difficult or very difficult and 33% were not able to correctly interpret at least one format. Correct interpretation was associated with preferred league table (OR = 1.62; 95% CI = 1.04–5.52) and if the data was presented in the preferred format. Medium and long education were associated with correct interpretation of at least one format (OR = 1.93; 95% CI = 1.16–3.21 and OR = 3.89; 95% CI = 1.90–7.95, respectively) while health literacy and cohabitation status were not. <b>Conclusions:</b> More than one third of the participants were not able to correctly interpret the data and the understanding of quality data improved with longer education and if the data was presented in the preferred format. Decision-makers should carefully consider displaying quality data according to preferred presentation format and to guide interpretation for individuals with short education.
DOI: 10.6084/m9.figshare.21749352.v2
title: Extensive genomic analysis in patients with <i>KRAS</i>-mutated solid tumors shows high frequencies of concurrent alterations and potential targets but has limited clinical impact

description: This study aimed to investigate the distribution and frequency of concurrent alterations in different cancers across <i>KRAS</i> subtypes and in different <i>KRAS</i> subtypes across cancers, and to identify potentially actionable targets and patients who received targeted treatment matched to their genomic profile (GP). In this descriptive and single-center study, we included 188 patients with solid tumors harboring <i>KRAS</i> mutations in codon 12, 13, 61, 117, or 146, referred to the Phase 1 Unit, Rigshospitalet, Copenhagen, Denmark from mid-2016 to 2020. Genomic co-alterations were detected with whole-exome sequencing, RNA sequencing, SNP array, and mRNA expression array on fresh biopsies. The study is part of the Copenhagen Prospective Personalized Oncology study (NCT02290522). The majority of patients had colorectal cancer (60.1%), non-small cell lung cancer (11.2%), or pancreatic cancer (10.6%). Most tumors were <i>KRAS</i>-mutated in codon 12 or 13 (93.7%) including G12D (27.1%), G12V (26.6%), G12C (11.7%), and G13D (11.2%). A total of 175 different co-alterations were found, most frequently pathogenic <i>APC</i> and <i>TP53</i> mutations (55.9% and 46.4%, respectively) and high expression of <i>CEACAM5</i> (73.4%). Different cancers and <i>KRAS</i> subtypes showed different patterns of co-alterations, and 157 tumors (83.5%) had potentially actionable targets with varying evidence of targetability (assessed using ESMO Scale for Clinical Actionability of molecular Targets). Of the 188 patients included in the study, 15 (7.4%) received treatment matched to their GP (e.g., immunotherapy and synthetic lethality drugs), of whom one had objective partial response according to Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. Performing extensive genomic analysis in patients with known <i>KRAS</i>-mutated solid tumors may contribute with information to the genomic landscape of cancers and identify targets for immunotherapy or synthetic lethality drugs, but currently appears to have overall limited clinical impact, as few patients received targeted therapy matched to their GP.
DOI: 10.6084/m9.figshare.21574680
title: Is it okay to choose to receive bad news by telephone? An observational study on psychosocial consequences of diagnostic workup for lung cancer suspicion

description: In-person meeting is considered the gold standard in current communication protocols regarding sensitive information, yet one size may not fit all, and patients increasingly demand or are offered disclosure of bad news by, e.g., telephone. It is unknown how patients’ active preference for communication modality affect psychosocial consequences of receiving potentially bad news. To explore psychosocial consequences in patients, who themselves chose to have results of lung cancer workup delivered either in-person or by telephone compared with patients randomly assigned to either delivery in a recently published randomised controlled trial (RCT). An observational study prospectively including patients referred for invasive workup for suspected lung cancer stratified in those declining (Patient’s Own Choice, POC group) and those participating in the RCT. On the day of invasive workup and five weeks later, patients completed a validated, nine-dimension, condition-specific questionnaire, Consequences of Screening in Lung Cancer (COS-LC). Primary outcome: difference in change in COS-LC dimensions between POC and RCT groups. In total, 151 patients were included in the POC group versus 255 in the RCT. Most (70%) in the POC group chose to have results by telephone. Baseline characteristics and diagnostic outcomes were comparable between POC and RCT groups, and in telephone and in-person subgroups too. We observed no statistically significant between-groups differences in any COS-LC score between POC and RCT groups, or between telephone and in-person subgroups in the POC group. Continually informed patients’ choice between in-person or telephone disclosure of results of lung cancer workup is not associated with differences in psychosocial outcomes. The present article supports further use of a simple model for how to prepare the patient for potential bad news.