cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7642310.v1
title: Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus <i>Caenorhabditis</i>

description: Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using transcriptomic data from the same larval stage of four <i>Caenorhabditis</i> species. The number of annotated lncRNAs in self-fertile nematodes was lower than in out-crossing species. We used a combination of approaches to identify putatively homologous lncRNAs: synteny, sequence conservation, and structural conservation. We classified a total of 1,532 out of 7,635 genes from the four species into families of lncRNAs with conserved synteny and expression at the larval stage, suggesting that a large fraction of the predicted lncRNAs may be species specific. Despite both sequence and local secondary structure seem to be poorly conserved, sequences within families frequently shared BLASTn hits and short sequence motifs, which were more likely to be unpaired in the predicted structures. We provide the first multi-species catalog of lncRNAs in nematodes and identify groups of lncRNAs with conserved synteny and expression, that share exposed motifs.
DOI: 10.7284/107341
title: Winch data collected during research cruise EN485 using a Markey DUSH-5 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642295
title: X-ray irradiation induces subtle changes in the genome-wide distribution of DNA hydroxymethylation with opposing trends in genic and intergenic regions

description: DNA hydroxymethylation has gained attention as an intermediate in the process of DNA demethylation. More recently, 5-hydroxymethylcytosine has been recognized as an independent epigenetic mark that can persist over time and that exerts influence on gene regulation and other biological processes. Deregulation of this DNA modification has been linked to tumorigenesis and a variety of other diseases. The impact of irradiation on DNA hydroxymethylation is poorly understood. In this study we exposed lung fibroblasts (IMR90) to 0.5 Gy and 2 Gy of X-rays, respectively. We characterized radiation induced changes of DNA hydroxymethylation 1 h, 6 h, 24 h and 120 h after exposure employing immunoprecipitation and subsequent deep sequencing of the genomic fraction enriched for hydroxymethylated DNA. Transcriptomic response to irradiation was analyzed for time points 6 h and 24 h post exposure by means of RNA sequencing. Irradiated and sham-irradiated samples shared the same overall distribution of 5-hydroxymethylcytosines with respect to genomic features such as promoters and exons. The frequency of 5-hydroxymethylcytosine peaks differentially detected in irradiated samples increased in genic regions over time, while the opposing trend was observed for intergenic regions. Onset and extent of this effect was dose dependent. Moreover, we demonstrated a biased distribution of 5-hmC alterations at CpG islands and sites occupied by the DNA binding protein CTCF. In summary, our study provides new insights into the epigenetic response to irradiation. Our data highlight genomic features more prone to irradiation induced changes of DNA hydroxymethylation, which might impact early and late onset effects of irradiation.
DOI: 10.6084/m9.figshare.7642298
title: The percentage of infant gaze following and heart rate levels from Physiological arousal predicts gaze following in infants

description: Data from twenty-five 10-month-old infants. In the baseline phase of each condition, the actress remained still for two seconds and then looked up gradually into the camera with both eyes closed. This was followed by the action phase, which differed between conditions. In the Eye Contact (EC) condition, the actress raised her eyes and looked into the camera for three seconds. In the No Cue (NC) condition, the actress closed her eyes for three seconds. In the Shivering (SV) condition, the model made a few rapid horizontal head shakes as if shivering for three seconds with closed eyes. The third phase was the Gazing phase. In this phase, the actress turned her head approximately 45° toward one of the two objects on the table and fixated on it for five seconds. In the NC and SV conditions, the actress opened her eyes just before shifting her head. All three conditions were run within-subject, and a total of 12 trials were presented to each infant. The principle measurement of gaze following was the infants first saccade toward an object during the gazing phase. If the infant looked at the same object the actress gazed at, their gaze behaviour was coded as gaze following. We separated the heart rate data from each of the three phases (Baseline, Action, and Gazing), and then we averaged the R-R intervals in each phase.
DOI: 10.6084/m9.figshare.7642301
title: Supplementary Text - Source from Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets

description: This R markdown file provides the source code used to generate the analyses and figures in the Supplementary Text, facilitating the reproduction of research results.
DOI: 10.6084/m9.figshare.7642301.v1
title: Supplementary Text - Source from Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets

description: This R markdown file provides the source code used to generate the analyses and figures in the Supplementary Text, facilitating the reproduction of research results.
DOI: 10.6084/m9.figshare.7642298.v1
title: The percentage of infant gaze following and heart rate levels from Physiological arousal predicts gaze following in infants

description: Data from twenty-five 10-month-old infants. In the baseline phase of each condition, the actress remained still for two seconds and then looked up gradually into the camera with both eyes closed. This was followed by the action phase, which differed between conditions. In the Eye Contact (EC) condition, the actress raised her eyes and looked into the camera for three seconds. In the No Cue (NC) condition, the actress closed her eyes for three seconds. In the Shivering (SV) condition, the model made a few rapid horizontal head shakes as if shivering for three seconds with closed eyes. The third phase was the Gazing phase. In this phase, the actress turned her head approximately 45° toward one of the two objects on the table and fixated on it for five seconds. In the NC and SV conditions, the actress opened her eyes just before shifting her head. All three conditions were run within-subject, and a total of 12 trials were presented to each infant. The principle measurement of gaze following was the infants first saccade toward an object during the gazing phase. If the infant looked at the same object the actress gazed at, their gaze behaviour was coded as gaze following. We separated the heart rate data from each of the three phases (Baseline, Action, and Gazing), and then we averaged the R-R intervals in each phase.
DOI: 10.7284/107267
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN486 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642283
title: All data from Phylogenetic investigation of skin sloughing rates in frogs: relationships with skin characteristics and disease-driven declines

description: Data utilized for analyses
DOI: 10.6084/m9.figshare.7642283.v1
title: All data from Phylogenetic investigation of skin sloughing rates in frogs: relationships with skin characteristics and disease-driven declines

description: Data utilized for analyses
DOI: 10.7284/108694
title: Fluorometer data collected during research cruise EN486 using a Turner 10-AU instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642268
title: Plasma protein biomarker measurements

description: Up to three replicates per protein per sample for 237 patients diagnosed with benign tumours, borderline or ovarian cancer stages I-IV. <br><br>Data has been generated in absolute concentrations with units given in the data file. <br><br>11 plasma protein biomarkers were quantified. <br>
DOI: 10.7284/103251
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN486 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642241
title: Supplementary Material for: Challenges and Opportunities for Cancer Predisposition Cascade Screening for Hereditary Breast and Ovarian Cancer and Lynch Syndrome in Switzerland: Findings from an International Workshop

description: <b><i>Background:</i></b> An international workshop on cancer predisposition cascade genetic screening for hereditary breast and ovarian cancer (HBOC) and Lynch syndrome (LS) took place in Switzerland, with leading researchers and clinicians in cascade screening and hereditary cancer from different disciplines. The purpose of the workshop was to enhance the implementation of cascade genetic screening in Switzerland. Participants discussed the challenges and opportunities associated with cascade screening for HBOC and LS in Switzerland (CASCADE study); family implications and the need for family-based interventions; the need to evaluate the cost-effectiveness of cascade genetic screening; and interprofessional collaboration needed to lead this initiative. <b><i>Methods:</i></b> The workshop aims were achieved through exchange of data and experiences from successful cascade screening programs in the Netherlands, Australia, and the state of Ohio, USA; Swiss-based studies and scientific experience that support cancer cascade screening in Switzerland; programs of research in psychosocial oncology and family-based studies; data from previous cost-effectiveness analyses of cascade genetic screening in the Netherlands and in Australia; and organizational experience from a large interprofessional collaborative. Scientific presentations were recorded and discussions were synthesized to present the workshop findings. <b><i>Results:</i></b> The key elements of successful implementation of cascade genetic screening are a supportive network of stakeholders and connection to complementary initiatives; sample size and recruitment of relatives; centralized organization of services; data-based cost-effectiveness analyses; transparent organization of the initiative; and continuous funding. <b><i>Conclusions:</i></b> This paper describes the processes and key findings of an international workshop on cancer predisposition cascade screening, which will guide the CASCADE study in Switzerland.
DOI: 10.6084/m9.figshare.7642247
title: Forelimb orientation and locomotion of sauropod dinosaurs: insights from the ?Middle Jurassic Tafaytour tracksites (Argana Basin, Morocco)

description: Forelimb posture in sauropod dinosaurs is still poorly understood. Although a laterally directed (semisupinated) manus is the plesiomorphic condition in sauropodomorphs, the sauropod track record prevailingly shows anterolateral to anterior manus orientations, suggesting a high degree of manus pronation. The ?Middle Jurassic Tafaytour tracksites described herein preserve at least 10 trackways, nine of which show laterally oriented, and in two examples even posterolaterally oriented, manual impressions. Located in the Argana Basin of the Western High Atlas, Morocco, the tracksite yields hundreds of footprints on a highly bioturbated surface, including examples with well-preserved digit and claw impressions. Footprint morphology and trackway configuration vary greatly between trackways. A literature review indicates that laterally directed manual impressions are restricted to small- and medium-sized trackmakers. Statistical analysis was performed on a larger sample (n = 79) of small sauropod trackways from around the world, indicating that lateral manual orientations are correlated with low locomotion speeds and narrow trackway gauges. Manus pronation in sauropods is hypothesized to occur when the forelimb is actively contributing to the propulsion of the animal, which would be the case at faster speeds or at wider trackway gauges where the center of mass is located more anteriorly. We present new approaches to the quantitative analysis of trackway data. Mean configuration plots allow for direct graphical comparisons of different trackways. Two types of trackway asymmetries are defined and quantified. The apparent glenoacetabular distance (GAD) represents a feasible proxy for body size, at least for the smaller sauropod trackmakers analyzed herein.
DOI: 10.6084/m9.figshare.7642256
title: Predatory hymenopteran assemblages in boreal Alaska: associations with forest composition and post-fire succession

description: Changes to the fire regime in boreal Alaska are shifting the ratio of coniferous to deciduous dominance on the landscape. The increase in aspen and birch may have important effects on predatory hymenopteran assemblages by providing a source of extrafloral nectar and increasing prey availability. Furthermore, fire-induced changes in successional age alter habitat structure and microclimate in ways that may favor ants. This study is the first to characterize the influence of fire-related vegetation changes on boreal predatory hymenopteran assemblages. We compare the abundance, species richness, and composition of predatory hymenopteran assemblages among forests at different stages of succession and of varying post-fire tree species compositions. Ant assemblages were weakly related to forest composition, but ants were significantly more abundant and speciose in early-successional forests than in mid-late successional forests. In contrast, macropterous wasp morphospecies richness and abundance, and micropterous wasp abundance, were positively related to the basal area of aspen, but were not related to successional stage. The results suggest that shifts in boreal vegetation related to climate warming will result in changes to the predaceous insect community, with ants responding positively to disturbance and wasps responding positively to an increase in the representation of aspen on the landscape.
DOI: 10.7284/107344
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN486 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111972
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN486 using a Trimble NT-300D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642241.v1
title: Supplementary Material for: Challenges and Opportunities for Cancer Predisposition Cascade Screening for Hereditary Breast and Ovarian Cancer and Lynch Syndrome in Switzerland: Findings from an International Workshop

description: <b><i>Background:</i></b> An international workshop on cancer predisposition cascade genetic screening for hereditary breast and ovarian cancer (HBOC) and Lynch syndrome (LS) took place in Switzerland, with leading researchers and clinicians in cascade screening and hereditary cancer from different disciplines. The purpose of the workshop was to enhance the implementation of cascade genetic screening in Switzerland. Participants discussed the challenges and opportunities associated with cascade screening for HBOC and LS in Switzerland (CASCADE study); family implications and the need for family-based interventions; the need to evaluate the cost-effectiveness of cascade genetic screening; and interprofessional collaboration needed to lead this initiative. <b><i>Methods:</i></b> The workshop aims were achieved through exchange of data and experiences from successful cascade screening programs in the Netherlands, Australia, and the state of Ohio, USA; Swiss-based studies and scientific experience that support cancer cascade screening in Switzerland; programs of research in psychosocial oncology and family-based studies; data from previous cost-effectiveness analyses of cascade genetic screening in the Netherlands and in Australia; and organizational experience from a large interprofessional collaborative. Scientific presentations were recorded and discussions were synthesized to present the workshop findings. <b><i>Results:</i></b> The key elements of successful implementation of cascade genetic screening are a supportive network of stakeholders and connection to complementary initiatives; sample size and recruitment of relatives; centralized organization of services; data-based cost-effectiveness analyses; transparent organization of the initiative; and continuous funding. <b><i>Conclusions:</i></b> This paper describes the processes and key findings of an international workshop on cancer predisposition cascade screening, which will guide the CASCADE study in Switzerland.
DOI: 10.6084/m9.figshare.7642247.v2
title: Forelimb orientation and locomotion of sauropod dinosaurs: insights from the ?Middle Jurassic Tafaytour tracksites (Argana Basin, Morocco)

description: Forelimb posture in sauropod dinosaurs is still poorly understood. Although a laterally directed (semisupinated) manus is the plesiomorphic condition in sauropodomorphs, the sauropod track record prevailingly shows anterolateral to anterior manus orientations, suggesting a high degree of manus pronation. The ?Middle Jurassic Tafaytour tracksites described herein preserve at least 10 trackways, nine of which show laterally oriented, and in two examples even posterolaterally oriented, manual impressions. Located in the Argana Basin of the Western High Atlas, Morocco, the tracksite yields hundreds of footprints on a highly bioturbated surface, including examples with well-preserved digit and claw impressions. Footprint morphology and trackway configuration vary greatly between trackways. A literature review indicates that laterally directed manual impressions are restricted to small- and medium-sized trackmakers. Statistical analysis was performed on a larger sample (n = 79) of small sauropod trackways from around the world, indicating that lateral manual orientations are correlated with low locomotion speeds and narrow trackway gauges. Manus pronation in sauropods is hypothesized to occur when the forelimb is actively contributing to the propulsion of the animal, which would be the case at faster speeds or at wider trackway gauges where the center of mass is located more anteriorly. We present new approaches to the quantitative analysis of trackway data. Mean configuration plots allow for direct graphical comparisons of different trackways. Two types of trackway asymmetries are defined and quantified. The apparent glenoacetabular distance (GAD) represents a feasible proxy for body size, at least for the smaller sauropod trackmakers analyzed herein.
DOI: 10.6084/m9.figshare.7642256.v2
title: Predatory hymenopteran assemblages in boreal Alaska: associations with forest composition and post-fire succession

description: Changes to the fire regime in boreal Alaska are shifting the ratio of coniferous to deciduous dominance on the landscape. The increase in aspen and birch may have important effects on predatory hymenopteran assemblages by providing a source of extrafloral nectar and increasing prey availability. Furthermore, fire-induced changes in successional age alter habitat structure and microclimate in ways that may favor ants. This study is the first to characterize the influence of fire-related vegetation changes on boreal predatory hymenopteran assemblages. We compare the abundance, species richness, and composition of predatory hymenopteran assemblages among forests at different stages of succession and of varying post-fire tree species compositions. Ant assemblages were weakly related to forest composition, but ants were significantly more abundant and speciose in early-successional forests than in mid-late successional forests. In contrast, macropterous wasp morphospecies richness and abundance, and micropterous wasp abundance, were positively related to the basal area of aspen, but were not related to successional stage. The results suggest that shifts in boreal vegetation related to climate warming will result in changes to the predaceous insect community, with ants responding positively to disturbance and wasps responding positively to an increase in the representation of aspen on the landscape.
DOI: 10.6084/m9.figshare.7642232
title: Context and perceptual asymmetry effects on the mismatch negativity (MMNm) to speech sounds: an MEG study

description: The mismatch negativity (MMN) of the auditory ERP/ERF has been shown to be sensitive to both phonetic and phonological contrasts. However, potential asymmetry effects and effects of the immediate phonetic contexts on this neural sensitivity are understudied phenomena. Using magnetoencephalography (MEG), we attempted to address this lacuna by investigating native Danish listeners’ MMNm to the phonological contrast between the consonants /t/ and /d/ in two different phonetic contexts in Danish: one word-initial, preserving the contrast’s phonemic status, and another word-final, neutralising it. We found no support for effects of the immediate phonetic context on the MMNm. However, we observed an asymmetry effect for the phonological contrast: Hearing [t] among [d]s elicited a significantly stronger MMNm than hearing [d] among [t]s. This asymmetry effect was mirrored in a behavioural oddball-detection task showing reduced sensitivity for hearing [d] among [t]s. We discuss both psychoacoustic aspects and phonological underspecification as potential explanations.
DOI: 10.6084/m9.figshare.7642256.v1
title: Predatory hymenopteran assemblages in boreal Alaska: associations with forest composition and post-fire succession

description: Changes to the fire regime in boreal Alaska are shifting the ratio of coniferous to deciduous dominance on the landscape. The increase in aspen and birch may have important effects on predatory hymenopteran assemblages by providing a source of extrafloral nectar and increasing prey availability. Furthermore, fire-induced changes in successional age alter habitat structure and microclimate in ways that may favor ants. This study is the first to characterize the influence of fire-related vegetation changes on boreal predatory hymenopteran assemblages. We compare the abundance, species richness, and composition of predatory hymenopteran assemblages among forests at different stages of succession and of varying post-fire tree species compositions. Ant assemblages were weakly related to forest composition, but ants were significantly more abundant and speciose in early-successional forests than in mid-late successional forests. In contrast, macropterous wasp morphospecies richness and abundance, and micropterous wasp abundance, were positively related to the basal area of aspen, but were not related to successional stage. The results suggest that shifts in boreal vegetation related to climate warming will result in changes to the predaceous insect community, with ants responding positively to disturbance and wasps responding positively to an increase in the representation of aspen on the landscape.
DOI: 10.7284/108689
title: Gyrocompass data collected during research cruise EN486 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition