cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4749175
title: Supplementary Data for Doctoral Thesis: Deep Learning Approaches for an Integrated Study of DNA Sequence, Epigenome and Chromatin Architecture

description: Supplementary Data for Doctoral Thesis: Deep Learning Approaches for an Integrated Study of DNA Sequence, Epigenome and Chromatin Architecture Appendix A lists all datasets used in constructing the chromatin feature compendia for the chromatin feature neural network training sets (deepHaem). Appendix B lists all CaptureC validation probes.
DOI: 10.5281/zenodo.4727147
title: Augmented emission maps: cold start maps for petrol vehicles (EU3-EU6)

description: In order to enable the sharing of data the emission data for vehicles is standardized. The data exchange format contains all data that is applicable for a specific engine taxonomy code. The standardized emission map has a “.map.txt” extension and is also human readable. The files starts with metadata which contains information about: the engine taxonomy code, total driven kilometers over which the data was gathered, total time in hours over which the data was gathered, the number of vehicles which were tested to create the emission map, the DOI (Digital Object Identifier) reference, Which emission maps are available in the file. The DOI 10.5281/zenodo refers to a meta-data document that provides the full description of the standardized emission map
DOI: 10.5281/zenodo.4727146
title: Augmented emission maps: cold start maps for petrol vehicles (EU3-EU6)

description: In order to enable the sharing of data the emission data for vehicles is standardized. The data exchange format contains all data that is applicable for a specific engine taxonomy code. The standardized emission map has a “.map.txt” extension and is also human readable. The files starts with metadata which contains information about: the engine taxonomy code, total driven kilometers over which the data was gathered, total time in hours over which the data was gathered, the number of vehicles which were tested to create the emission map, the DOI (Digital Object Identifier) reference, Which emission maps are available in the file. The DOI 10.5281/zenodo refers to a meta-data document that provides the full description of the standardized emission map
DOI: 10.5281/zenodo.4727150
title: Augmented emission maps: cold start maps for diesel vehicles (EU4-EU6)

description: In order to enable the sharing of data the emission data for vehicles is standardized. The data exchange format contains all data that is applicable for a specific engine taxonomy code. The standardized emission map has a “.map.txt” extension and is also human readable. The files starts with metadata which contains information about: the engine taxonomy code, total driven kilometers over which the data was gathered, total time in hours over which the data was gathered, the number of vehicles which were tested to create the emission map, the DOI (Digital Object Identifier) reference, Which emission maps are available in the file. The DOI 10.5281/zenodo refers to a meta-data document that provides the full description of the standardized emission map
DOI: 10.5281/zenodo.4727149
title: Augmented emission maps: cold start maps for diesel vehicles (EU4-EU6)

description: In order to enable the sharing of data the emission data for vehicles is standardized. The data exchange format contains all data that is applicable for a specific engine taxonomy code. The standardized emission map has a “.map.txt” extension and is also human readable. The files starts with metadata which contains information about: the engine taxonomy code, total driven kilometers over which the data was gathered, total time in hours over which the data was gathered, the number of vehicles which were tested to create the emission map, the DOI (Digital Object Identifier) reference, Which emission maps are available in the file. The DOI 10.5281/zenodo refers to a meta-data document that provides the full description of the standardized emission map
DOI: 10.5281/zenodo.4749173
title: Dataset related to article "New methodology based on freeze-drying for long-term preservation of human sperm"

description: This record contains raw data related to article “New methodology based on freeze-drying for long-term preservation of human sperm" Freeze-drying is an ecological non-cryogenic storage solution that could represent an economic tool to transport sperm all over the world. This methodology was applied only to mice and a few other species so far, but not for a long-term storage of human sperm. For the first time we investigated whether freeze-drying could deteriorate human sperm DNA fragmentation at different time points (1 month, 3 months and 10 months). We used a high concentration of trehalose in the freeze-drying buffer and 2 vials per time point were insufflated with argon, replacing oxygen, and stored at 4°C or room temperature; the remaining 2 vials were stored in normal atmosphere at the same temperature conditions. We did not observe any statistically significant difference between the groups analyzed, suggesting that our lyophilization solution could maintain unaltered sperm DNA fragmentation until 10 months of storage without the presence of a high vacuum. These evidences support the potential use of freeze-drying also for human sperm in fertility clinics. <strong>Correspondence:</strong> Stefano Castellano, Division of Gynecology and Reproductive Medicine, Department of Gynecology, Fertility Center, Humanitas Research Hospital – IRCCS, Via Alessandro Manzoni 56, 20089, Rozzano, Milan, Italy (mobile: +393347401507, email: stefano.castellano@humanitas.it)
DOI: 10.5281/zenodo.4749172
title: Dataset related to article "New methodology based on freeze-drying for long-term preservation of human sperm"

description: This record contains raw data related to article “New methodology based on freeze-drying for long-term preservation of human sperm" Freeze-drying is an ecological non-cryogenic storage solution that could represent an economic tool to transport sperm all over the world. This methodology was applied only to mice and a few other species so far, but not for a long-term storage of human sperm. For the first time we investigated whether freeze-drying could deteriorate human sperm DNA fragmentation at different time points (1 month, 3 months and 10 months). We used a high concentration of trehalose in the freeze-drying buffer and 2 vials per time point were insufflated with argon, replacing oxygen, and stored at 4°C or room temperature; the remaining 2 vials were stored in normal atmosphere at the same temperature conditions. We did not observe any statistically significant difference between the groups analyzed, suggesting that our lyophilization solution could maintain unaltered sperm DNA fragmentation until 10 months of storage without the presence of a high vacuum. These evidences support the potential use of freeze-drying also for human sperm in fertility clinics. <strong>Correspondence:</strong> Stefano Castellano, Division of Gynecology and Reproductive Medicine, Department of Gynecology, Fertility Center, Humanitas Research Hospital – IRCCS, Via Alessandro Manzoni 56, 20089, Rozzano, Milan, Italy (mobile: +393347401507, email: stefano.castellano@humanitas.it)
DOI: 10.6084/m9.figshare.14573002.v1
title: Social Network Construction from Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food-caching bird

description: Code to construct a social network from feeder visitation data
DOI: 10.6084/m9.figshare.14573005.v1
title: NBDA from Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food-caching bird

description: Code for network-based diffusion analysis of novel feeder discovery data
DOI: 10.6084/m9.figshare.14573005
title: NBDA from Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food-caching bird

description: Code for network-based diffusion analysis of novel feeder discovery data
DOI: 10.6084/m9.figshare.14573014.v1
title: Cognitive Testing Analysis from Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food-caching bird

description: Code for determining spatial cognition and reversal spatial cognition scores from feeder visitation data
DOI: 10.6084/m9.figshare.14573002
title: Social Network Construction from Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food-caching bird

description: Code to construct a social network from feeder visitation data
DOI: 10.6084/m9.figshare.14573011.v1
title: Novel Feeder Discovery from Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food-caching bird

description: Code to analyze novel feeder discovery and construct figures
DOI: 10.6084/m9.figshare.14573011
title: Novel Feeder Discovery from Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food-caching bird

description: Code to analyze novel feeder discovery and construct figures
DOI: 10.6084/m9.figshare.14573014
title: Cognitive Testing Analysis from Food discovery is associated with different reliance on social learning and lower cognitive flexibility across environments in a food-caching bird

description: Code for determining spatial cognition and reversal spatial cognition scores from feeder visitation data
DOI: 10.3886/e120570v1-86240
title: Data and Code for: The Legacy of Colonial Medicine in Central Africa

description: Between 1921 and 1956, French colonial governments organized medical campaigns to treat and prevent sleeping sickness. Villagers were forcibly examined and injected with medications with severe, sometimes fatal, side effects. We digitized thirty years of archival records to document the locations of campaign visits at a granular geographic level for five central African countries. We find that greater campaign exposure reduces vaccination rates and trust in medicine -- as measured by willingness to consent to a blood test. We examine relevance for present day health initiatives; World Bank projects in the health sector are less successful in areas with greater exposure.
DOI: 10.6084/m9.figshare.14573043
title: Supplementary Material for: Reinforcement Effects of Social Network Intervention during Nutritional Supplementation in Frail Older Adults

description: <b><i>Introduction:</i></b> Chronic undernutrition and a homebound state are corelated and are both important components of frailty. However, whether social network intervention combined with protein supplementation is an effective strategy to prevent functional decline among frail older adults is unclear. <b><i>Methods:</i></b> 150 frail older adults participated in a 3-month, 3-armed, community-based clinical trial and were randomly assigned to one of 3 groups: high-protein supplementation (additional 27 g of protein/day), the Social Nutrition Program (additional 27 g of protein/day and social network intervention), or a control group. Those assigned to the Social Nutrition Program group received individual counseling from 1 dietitian and 1 social worker during 6 home visits and were encouraged to participate in 4 sessions of community-based cooking activities, the social kitchen program. Primary outcomes were changes in Physical Functioning (PF) and the Timed Up and Go (TUG) test and were assessed at 0 months (baseline), 1.5 months (interim), and 3, 6, and 9 months (postintervention). <b><i>Results:</i></b> Compared with the control group, participants in the Social Nutrition Program showed an average improvement of 2.2–3.0 s in the TUG test and this improvement persisted for 3 months after the end of the program (post hoc <i>p</i> ≤ 0.030). The Social Nutrition Program also increased PF by 1.3 points while the control group showed a 1.4 point reduction at the end of the program (post hoc <i>p</i> = 0.045). Improvement in PF and TUG results was primarily observed for the socially frail subgroup of older adults in the Social Nutrition Program group rather than the physically frail subgroup. Frequency of leaving home functioned as a mediator (<i>p</i> = 0.042) and explained 31.2% of the total effect of the Social Nutrition Program on PF change. <b><i>Conclusion:</i></b> Our results indicate that social network intervention combined with protein supplementation can improve both the magnitude and duration of functional status among frail older community-dwelling adults.
DOI: 10.6084/m9.figshare.14573043.v1
title: Supplementary Material for: Reinforcement Effects of Social Network Intervention during Nutritional Supplementation in Frail Older Adults

description: <b><i>Introduction:</i></b> Chronic undernutrition and a homebound state are corelated and are both important components of frailty. However, whether social network intervention combined with protein supplementation is an effective strategy to prevent functional decline among frail older adults is unclear. <b><i>Methods:</i></b> 150 frail older adults participated in a 3-month, 3-armed, community-based clinical trial and were randomly assigned to one of 3 groups: high-protein supplementation (additional 27 g of protein/day), the Social Nutrition Program (additional 27 g of protein/day and social network intervention), or a control group. Those assigned to the Social Nutrition Program group received individual counseling from 1 dietitian and 1 social worker during 6 home visits and were encouraged to participate in 4 sessions of community-based cooking activities, the social kitchen program. Primary outcomes were changes in Physical Functioning (PF) and the Timed Up and Go (TUG) test and were assessed at 0 months (baseline), 1.5 months (interim), and 3, 6, and 9 months (postintervention). <b><i>Results:</i></b> Compared with the control group, participants in the Social Nutrition Program showed an average improvement of 2.2–3.0 s in the TUG test and this improvement persisted for 3 months after the end of the program (post hoc <i>p</i> ≤ 0.030). The Social Nutrition Program also increased PF by 1.3 points while the control group showed a 1.4 point reduction at the end of the program (post hoc <i>p</i> = 0.045). Improvement in PF and TUG results was primarily observed for the socially frail subgroup of older adults in the Social Nutrition Program group rather than the physically frail subgroup. Frequency of leaving home functioned as a mediator (<i>p</i> = 0.042) and explained 31.2% of the total effect of the Social Nutrition Program on PF change. <b><i>Conclusion:</i></b> Our results indicate that social network intervention combined with protein supplementation can improve both the magnitude and duration of functional status among frail older community-dwelling adults.
DOI: 10.5281/zenodo.4749206
title: Seafloor output from the MEDUSA model

description: - Output from the MEDUSA model (Yool et al., GMD, 2013) - NEMO resolution 1/4-degree - Simulation performed as part of the ROAM project (UK Ocean Acidification Research Programme) - CMIP5 Historical and RCP 8.5 extension (1975-2099 inclusive) - Simulation described in Yool et al., JGR, 2015 - Subset of output prepared for Mission Atlantic project by A. Yool in April 2021 - Seafloor fields of physical and biogeochemical properties for the periods 2016-2025 and 2090-2099 - Note that this is test output produced for a specific purpose
description: THIS IS TEST OUTOUT
DOI: 10.5281/zenodo.4749264
title: The restoration potential of fynbos riparian seed banks following alien clearing

description: Riparian areas contribute significantly to the spread of many invasive alien tree species which alter the ecosystem by bringing about significant water loss and changing the natural flow regimes of the system. For this reason, many alien clearing initiatives initially focus on riparian areas but limited resources allows for little restoration to these areas after clearing. The aim of this project was to assess the composition and viability of riparian seed banks before and after invasion to be used by conservation managers and land-owners in assessing post-disturbance restoration requirements. The focus was on riparian seed bank composition in four river systems in the south-western part of the Western Cape province (the Berg, Eerste, Molenaars and Wit Rivers). Equal number of plots were selected in both relatively un-invaded (&lt;25% IAP cover) and invaded (&gt;75% IAP cover) sections of the rivers. The seedlings that emerged from the soil samples were compared in terms of diversity, species richness, similarity and assembly groupings. Findings show that invasion alters the assembly patterns within riparian seed banks. Species richness, diversity and similarity of species showed no clear pattern and was suggested to be site specific. It is suggested that after intesive alien infestation, restoration will only be successfull if a seed source is restored by re-planting certain key riparian tree species that are not present in the seed bank and follow-up treatements continue.
description: To evaluate the restoration potential of riparian seed banks after invasion
DOI: 10.5281/zenodo.4749263
title: The restoration potential of fynbos riparian seed banks following alien clearing

description: Riparian areas contribute significantly to the spread of many invasive alien tree species which alter the ecosystem by bringing about significant water loss and changing the natural flow regimes of the system. For this reason, many alien clearing initiatives initially focus on riparian areas but limited resources allows for little restoration to these areas after clearing. The aim of this project was to assess the composition and viability of riparian seed banks before and after invasion to be used by conservation managers and land-owners in assessing post-disturbance restoration requirements. The focus was on riparian seed bank composition in four river systems in the south-western part of the Western Cape province (the Berg, Eerste, Molenaars and Wit Rivers). Equal number of plots were selected in both relatively un-invaded (&lt;25% IAP cover) and invaded (&gt;75% IAP cover) sections of the rivers. The seedlings that emerged from the soil samples were compared in terms of diversity, species richness, similarity and assembly groupings. Findings show that invasion alters the assembly patterns within riparian seed banks. Species richness, diversity and similarity of species showed no clear pattern and was suggested to be site specific. It is suggested that after intesive alien infestation, restoration will only be successfull if a seed source is restored by re-planting certain key riparian tree species that are not present in the seed bank and follow-up treatements continue.
description: To evaluate the restoration potential of riparian seed banks after invasion
DOI: 10.17632/2v25frvmvs.1
title: Distinct pathogenic genes causing intellectual disability and autism exhibit a common neuronal network hyperactivity phenotype

description: Pathogenic mutations in either one of the epigenetic modifiers EHMT1, MBD5, MLL3 or SMARCB1 have been identified to be causative for Kleefstra syndrome spectrum (KSS), a neurodevelopmental disorder with clinical features of both intellectual disability (ID) and autism spectrum disorder (ASD). To understand how these variants lead to the phenotypic convergence in KSS we employed a loss of function approach to assess neuronal network development at the molecular, single cell and network activity level. KSS-gene deficient neuronal networks all developed into hyperactive networks with altered network organization and excitatory-inhibitory balance. Interestingly, even though transcriptional data revealed distinct regulatory mechanisms, KSS-target genes share similar functions in regulating neuronal excitability and synaptic function, several of which are associated with ID and ASD. Our results show that KSS-genes mainly converge at the level of neuronal network communication, providing new insights into the pathophysiology of KSS and phenotypically congruent disorders.
DOI: 10.6084/m9.figshare.14573082
title: data.xlsx

description: Impact of ventilation modes on bronchoscopic Chartis assessment outcome in candidates for endobronchial valve treatment
DOI: 10.6084/m9.figshare.14573082.v1
title: data.xlsx

description: Impact of ventilation modes on bronchoscopic Chartis assessment outcome in candidates for endobronchial valve treatment
DOI: 10.5281/zenodo.4749257
title: Effects of Chromolaena odorata on mammalian biodiversity in Hluhluwe-iMfolozi Park, South Africa

description: This study investigated the effects of the Triffid weed Chromolaena odorata on small and large mammals in Hluhluwe-iMfolozi Park. C. odorata is a widespread invasive alien plant that poses threat to the highly maintained natural vegetation in HiP and most other protected areas in KwaZulu-Natal. Following the opinion that the effects of invasive alien plants on all levels of biodiversity need to be recognised for their effective control, we compared small and large mammal species richness and diversity between areas with differing C. odorata invasion durations, areas with differing clearing times and an area with no history of invasion as a control area. Small mammal trapping was done using Sherman live traps and mark-recapture techniques. Track counts were used to estimate large mammal species abundance, richness and diversity. The control area had higher small mammal species richness and diversity than the invaded areas, which suggests that invaded areas were not suitable habitats for small mammals. It was also found that small and large mammal species richness and diversity decreased with the increase in invasion duration, which shows that the more time C. odorata is left to establish the more disturbance it causes to the habitat. We found the uninvaded treatment to have the highest diversity of large mammal species than all the invaded treatments, which suggests that large mammalian species show some degree of avoidance to the invaded areas. We also found that there were significant differences between the treatments with regard to large mammal species diversity indices. Some of the large mammalian species appeared to neither avoid nor prefer invaded areas. It is hypothesized that they use invaded areas to hide away from predators as most of them fall prey to many carnivores. Also, C. odorata invaded areas could provide suitable shelter from climatic extremes. The treatments cleared of C. odorata showed an increase in both small and large mammalian species richness and diversity, suggesting that clearing of this plant helps in rehabilitation of the ecosystem. However, large mammal species composition in the cleared treatments remained different to pre-invasion state, which suggests that the habitat may remain changed for a long time after clearing. Managers of conservation areas should therefore prioritise alien plant removal in order to maintain healthy ecosystems.