cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1579605
title: Genome-wide analysis of microsatellite markers based on the sequenced database of Chinese spring wheat (Triticum aestivum L.)

description: Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker assisted breeding of crops. Although a draft sequence for hexaploid bread wheat is available, to date, there is no published systemic analysis of SSRs in wheat. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution of wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.
DOI: 10.6084/m9.figshare.1579599
title: Multi-Layered Mind Map

description: Mind Map of current knowledge on Biodiversity (BD)- Ecosystem Functions (EF)- Ecosystem Services (ES)- Human Well Being (HWB) research. The Mind Map was created using XMind 6 Free (v3.5.1) open source mind mapping brainstorming and productivity software tool (https://www.xmind.net/). Further information on the methodology and techniques used as well as a short note explaining how to access it and how to extract information can be found at Pascual et al., 2016. (Ecosystem Services, Volume 17, Pages 112–122).Paper source must be cited if the entire or part of the data contained here is to be used for future publications (Cite: Pascual, M., Pérez Miñana, E., Giacomello, E. (2016). Integrating knowledge on biodiversity and ecosystem services: Mind-mapping and Bayesian Network modelling. Ecosystem Services 16: 112-122. doi:10.1016/j.ecoser.2015.12.004
DOI: 10.6084/m9.figshare.1579595
title: Narrowing Down On CIPK16 Orthologues: A Gene Involved In Enhanced Salt Tolerance

description: Calcineurin B-Like Protein Interacting Protein Kinases (CIPKs) are key regulators of pre-transcriptional and post-translational responses to abiotic stresses. Many plant species have numerous forms of CIPKs, which appear to have very specific roles during abiotic stress. From a forward genetics screen, Arabidopsis thaliana CIPK16 (AtCIPK16) has been previously identified as an important gene responsible for reduced shoot salt accumulation and improved salinity tolerance in Arabidopsis and transgenic barley. However, the existence of AtCIPK16 homologues in cereals and the mode of action of AtCIPK16 in them are still unknown. Thus, this study aimed to understand the prevalence of CIPK16, and in return find an AtCIPK16 orthologue in cereals. A phylogenetic analysis has been performed on CIPK genes obtained from several species related to A. thaliana and cereal crops. The resulting phylogenetic tree revealed insights into the evolution of CIPK16 which has important consequences for breeding salt tolerance in cereal crops. One particular observation was that the clade including AtCIPK16 had a sister clade which contained two segmentally duplicated genes AtCIPK5 and AtCIPK25. Furthermore, we find AtCIPK16 contains an indel which is conserved in Brassicaceae.
DOI: 10.6084/m9.figshare.1579597
title: BN Details

description: Partitioned expressions used in the nodes to specify their NPTs as well as details of all the scenarios used in the BN Model of Pascual et al., 2016 (Ecosystem Services, Volume 17, Pages 112-122).Paper source must be cited if the entire or part of the data contained here is to be used for future publications (Cite: Pascual, M., Pérez Miñana, E., Giacomello, E. (2016). Integrating knowledge on biodiversity and ecosystem services: Mind-mapping and Bayesian Network modelling. Ecosystem Services 16: 112-122. doi:10.1016/j.ecoser.2015.12.004
DOI: 10.6084/m9.figshare.1579599.v1
title: Multi-Layered Mind Map

description: Mind Map of current knowledge on Biodiversity (BD)- Ecosystem Functions (EF)- Ecosystem Services (ES)- Human Well Being (HWB) research. The Mind Map was created using XMind 6 Free (v3.5.1) open source mind mapping brainstorming and productivity software tool (https://www.xmind.net/). Further information on the methodology and techniques used as well as a short note explaining how to access it and how to extract information can be found at Pascual et al., 2016. (Ecosystem Services, Volume 17, Pages 112–122).Paper source must be cited if the entire or part of the data contained here is to be used for future publications (Cite: Pascual, M., Pérez Miñana, E., Giacomello, E. (2016). Integrating knowledge on biodiversity and ecosystem services: Mind-mapping and Bayesian Network modelling. Ecosystem Services 16: 112-122. doi:10.1016/j.ecoser.2015.12.004
DOI: 10.6084/m9.figshare.1579595.v1
title: Narrowing Down On CIPK16 Orthologues: A Gene Involved In Enhanced Salt Tolerance

description: Calcineurin B-Like Protein Interacting Protein Kinases (CIPKs) are key regulators of pre-transcriptional and post-translational responses to abiotic stresses. Many plant species have numerous forms of CIPKs, which appear to have very specific roles during abiotic stress. From a forward genetics screen, Arabidopsis thaliana CIPK16 (AtCIPK16) has been previously identified as an important gene responsible for reduced shoot salt accumulation and improved salinity tolerance in Arabidopsis and transgenic barley. However, the existence of AtCIPK16 homologues in cereals and the mode of action of AtCIPK16 in them are still unknown. Thus, this study aimed to understand the prevalence of CIPK16, and in return find an AtCIPK16 orthologue in cereals. A phylogenetic analysis has been performed on CIPK genes obtained from several species related to A. thaliana and cereal crops. The resulting phylogenetic tree revealed insights into the evolution of CIPK16 which has important consequences for breeding salt tolerance in cereal crops. One particular observation was that the clade including AtCIPK16 had a sister clade which contained two segmentally duplicated genes AtCIPK5 and AtCIPK25. Furthermore, we find AtCIPK16 contains an indel which is conserved in Brassicaceae.
DOI: 10.6084/m9.figshare.1579594
title: Committed CO2 emissions

description: Plot shows the future trend in global annual CO2 emissions that can be anticipated to come from existing energy and transportation infrastructure by industry sector (as of 2010). Numbers in shaded areas are in cumulative Gt of CO2
DOI: 10.6084/m9.figshare.1579586
title: Behavioral data and histograms

description: This spreadsheet contains the results of each behavioral test performed. It also contains the calculated values of mean and SEM values for performance by each treatment group for each time point. The histograms featured in the publication are also included in the spreadsheet. Please refer to the page descriptions for the type of test performed.
DOI: 10.6084/m9.figshare.1579580
title: Focus Groups on Source Water Quality

description: Transcripts from focus groups conducted with members of the public in 4 communities across British Columbia, Canada.
DOI: 10.6084/m9.figshare.1579586.v1
title: Behavioral data and histograms

description: This spreadsheet contains the results of each behavioral test performed. It also contains the calculated values of mean and SEM values for performance by each treatment group for each time point. The histograms featured in the publication are also included in the spreadsheet. Please refer to the page descriptions for the type of test performed.
DOI: 10.6084/m9.figshare.1579568
title: Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells

description: ABSTRACTThe human genome contains some thousands of long non coding RNAs (lncRNAs). Many of these transcripts are presently considered crucial regulators of gene expression and functionally implicated in developmental processes in Eukaryotes. Notably, despite a huge number of lncRNAs are expressed in the Central Nervous System (CNS), only a few of them have been characterized in terms of molecular structure, gene expression regulation and function. In the present study, we identify linc-NeD125 as a novel cytoplasmic, neuronal-induced long intergenic non coding RNA (lincRNA). Linc-NeD125 represents the host gene for miR-125b-1, a microRNA with an established role as negative regulator of human neuroblastoma cell proliferation. Here, we demonstrate that these two overlapping non coding RNAs are coordinately induced during <i>in vitro</i> neuronal differentiation, and that their expression is regulated by different mechanisms. While the production of miR-125b-1 relies on transcriptional regulation, linc-NeD125 is controlled at the post-transcriptional level, through modulation of its stability.We also demonstrate that linc-NeD125 functions independently of the hosted microRNA, by reducing cell proliferation and activating the antiapoptotic factor BCL-2.
DOI: 10.6084/m9.figshare.1579580.v1
title: Focus Groups on Source Water Quality

description: Transcripts from focus groups conducted with members of the public in 4 communities across British Columbia, Canada.
DOI: 10.6084/m9.figshare.1579567
title: Learning SPARQL Chapter 2: RDF background (complete)

description: This is presentation for the Vanderbilt Heard Library group discussing the book Learning SPARQL by Bob DuCharme. It is a presentation which covers chapter 2. Topics include RDF as a data model and serializations, common human-readable descriptive properties, Linked Data, and entailment.
DOI: 10.6084/m9.figshare.1579568.v1
title: Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells

description: ABSTRACTThe human genome contains some thousands of long non coding RNAs (lncRNAs). Many of these transcripts are presently considered crucial regulators of gene expression and functionally implicated in developmental processes in Eukaryotes. Notably, despite a huge number of lncRNAs are expressed in the Central Nervous System (CNS), only a few of them have been characterized in terms of molecular structure, gene expression regulation and function. In the present study, we identify linc-NeD125 as a novel cytoplasmic, neuronal-induced long intergenic non coding RNA (lincRNA). Linc-NeD125 represents the host gene for miR-125b-1, a microRNA with an established role as negative regulator of human neuroblastoma cell proliferation. Here, we demonstrate that these two overlapping non coding RNAs are coordinately induced during <i>in vitro</i> neuronal differentiation, and that their expression is regulated by different mechanisms. While the production of miR-125b-1 relies on transcriptional regulation, linc-NeD125 is controlled at the post-transcriptional level, through modulation of its stability.We also demonstrate that linc-NeD125 functions independently of the hosted microRNA, by reducing cell proliferation and activating the antiapoptotic factor BCL-2.
DOI: 10.6084/m9.figshare.1579567.v1
title: Learning SPARQL Chapter 2: RDF background (complete)

description: This is presentation for the Vanderbilt Heard Library group discussing the book Learning SPARQL by Bob DuCharme. It is a presentation which covers chapter 2. Topics include RDF as a data model and serializations, common human-readable descriptive properties, Linked Data, and entailment.
DOI: 10.6084/m9.figshare.1579554
title: The cell ratchet: Interplay between efficient protrusions and adhesion determines cell motion

description: Many physiological and pathological processes involve directed cell motion. In general, migrating cells are represented with a polarized morphology with extending and retracting protrusions at the leading edge. However, cell motion is a more complex phenomenon. Cells show heterogeneous morphologies and high protrusive dynamics is not always related to cell shape. This prevents the quantitative prediction of cell motion and the identification of cellular mechanisms setting directionality. Here we discuss the importance of protrusion fluctuations in directed cell motion. We show how their spatiotemporal distribution and dynamics determine the fluctuations and directions of cell motion for NIH3T3 fibroblasts plated on micro-patterned adhesive <i>ratchets</i>.<sup>1</sup> We introduce <i>efficient protrusions</i> and <i>direction index</i> which capture short-term cell motility over hours: these new read-outs allow the prediction of parameters characteristic for the long-term motion of cells over days. The results may have important implications for the study of biological phenomena where directed cell migration is involved, in morphogenesis and in cancer.
DOI: 10.6084/m9.figshare.1579554.v1
title: The cell ratchet: Interplay between efficient protrusions and adhesion determines cell motion

description: Many physiological and pathological processes involve directed cell motion. In general, migrating cells are represented with a polarized morphology with extending and retracting protrusions at the leading edge. However, cell motion is a more complex phenomenon. Cells show heterogeneous morphologies and high protrusive dynamics is not always related to cell shape. This prevents the quantitative prediction of cell motion and the identification of cellular mechanisms setting directionality. Here we discuss the importance of protrusion fluctuations in directed cell motion. We show how their spatiotemporal distribution and dynamics determine the fluctuations and directions of cell motion for NIH3T3 fibroblasts plated on micro-patterned adhesive <i>ratchets</i>.<sup>1</sup> We introduce <i>efficient protrusions</i> and <i>direction index</i> which capture short-term cell motility over hours: these new read-outs allow the prediction of parameters characteristic for the long-term motion of cells over days. The results may have important implications for the study of biological phenomena where directed cell migration is involved, in morphogenesis and in cancer.
DOI: 10.6084/m9.figshare.1579463
title: Wireless rat EEG recordings inside a water maze

description: This dataset contains local field potential (LFP) recordings obtained from the hippocampus and striatum of rats, as they undertook a water maze task. Each of the enclosed zip folders contains 1) a Matlab data file containing the artifact-processed LFP, and 2) text file describing the data organisation. Local-field potential data is shown for the following experimental phases: pre-maze, water-maze, platform.
DOI: 10.6084/m9.figshare.1579462
title: Multiple obstacle avoidance of four-wheeled vehicle with steering limitation using nondifferentiable control Lyapunov function

description: Controlling a mobile robot in a space with obstacles is a well-known problem in robotics. The control objective is for the mobile robot to reach a goal point with obstacle avoidance. In this paper, we specially consider the multiple obstacle avoidance problem for particularly a four-wheeled vehicle. Assuming that the shapes and locations of the obstacles are known, we propose a design method of a nondifferentiable navigation function, which guides a vehicle at the desired point. The control law for the four-wheeled vehicle is obtained from the extended function of the navigation function. As four-wheeled vehicles cannot move sideways because of their nonholonomic constraint, the proposed control law addresses this difficulty by considering a decrease in the control Lyapunov function, and can be applied to vehicles with steering limitations. Moreover, the control law makes it possible for the vehicles to achieve an -point turn automatically without the need for any rule-based decision-making or heuristic method. The four-wheeled vehicle can reach the goal point from any initial point under the proposed control law. Our experimental results with a small four-wheeled vehicle are presented at the end of this paper.
DOI: 10.6084/m9.figshare.1579457
title: How fast do objects fall in visual memory?

description: 5 (task – mouse gain [blocked]) × 2 (motion direction) × 3 (vanishing position) × 6 (retention interval)
DOI: 10.6084/m9.figshare.1579462.v1
title: Multiple obstacle avoidance of four-wheeled vehicle with steering limitation using nondifferentiable control Lyapunov function

description: Controlling a mobile robot in a space with obstacles is a well-known problem in robotics. The control objective is for the mobile robot to reach a goal point with obstacle avoidance. In this paper, we specially consider the multiple obstacle avoidance problem for particularly a four-wheeled vehicle. Assuming that the shapes and locations of the obstacles are known, we propose a design method of a nondifferentiable navigation function, which guides a vehicle at the desired point. The control law for the four-wheeled vehicle is obtained from the extended function of the navigation function. As four-wheeled vehicles cannot move sideways because of their nonholonomic constraint, the proposed control law addresses this difficulty by considering a decrease in the control Lyapunov function, and can be applied to vehicles with steering limitations. Moreover, the control law makes it possible for the vehicles to achieve an -point turn automatically without the need for any rule-based decision-making or heuristic method. The four-wheeled vehicle can reach the goal point from any initial point under the proposed control law. Our experimental results with a small four-wheeled vehicle are presented at the end of this paper.
DOI: 10.6084/m9.figshare.1579463.v1
title: Wireless rat EEG recordings inside a water maze

description: This dataset contains local field potential (LFP) recordings obtained from the hippocampus and striatum of rats, as they undertook a water maze task. Each of the enclosed zip folders contains 1) a Matlab data file containing the artifact-processed LFP, and 2) text file describing the data organisation. Local-field potential data is shown for the following experimental phases: pre-maze, water-maze, platform.
DOI: 10.6084/m9.figshare.1579457.v1
title: How fast do objects fall in visual memory?

description: 5 (task – mouse gain [blocked]) × 2 (motion direction) × 3 (vanishing position) × 6 (retention interval)
DOI: 10.6084/m9.figshare.1579442
title: Data & materials for Moutsiana et al (2016)

description: This archive contains stimulus presentation and analysis code as well as the data from behavioural experiments in our study 'Cortical idiosyncrasies predict the perception of object size' by Moutsiana et al. (2016 Nat Commun). Processed pRF data from the neuroimaging experiments are available on Zenodo.
DOI: 10.6084/m9.figshare.1579443
title: Teaching introductory GIS programming to geographers using an open source Python approach

description: Computer programming is not commonly taught to geographers as a part of geographic information system (GIS) courses, but the advent of NeoGeography, big data and open GIS means that programming skills are becoming more important. To encourage the teaching of programming to geographers, this paper outlines a course based around a series of laboratories that aims to provide an introduction to programming. Methods for teaching and assessment are recommended. These laboratories use core spatial concepts that are relevant for all areas of geographic study, and use an open source Python approach that has wider logistical and pedagogical benefits.
DOI: 10.6084/m9.figshare.1579443.v1
title: Teaching introductory GIS programming to geographers using an open source Python approach

description: Computer programming is not commonly taught to geographers as a part of geographic information system (GIS) courses, but the advent of NeoGeography, big data and open GIS means that programming skills are becoming more important. To encourage the teaching of programming to geographers, this paper outlines a course based around a series of laboratories that aims to provide an introduction to programming. Methods for teaching and assessment are recommended. These laboratories use core spatial concepts that are relevant for all areas of geographic study, and use an open source Python approach that has wider logistical and pedagogical benefits.
DOI: 10.6084/m9.figshare.1579439
title: Decision-making of Prefrontal Patients with the Iowa Gambling Task: Unexpected Spared Performances and Preliminary Evidence for the Need of Alternative Measures

description: <i>Objective.</i> Human decision-making is a growing area of research most commonly associated with the Iowa Gambling Task (IGT), which was first developed to assess patients with prefrontal cortex (PFC) damage. The IGT is now considered an appropriate task to predict behavioral disorders in various clinical populations. However, several studies have questioned the validity and reliability of the task, arguing that its particular payoff scheme may influence the decision-making process in terms of sensitivity to gain-loss frequency (GLF) rather than long-term outcome (the basic assumption of IGT). Despite the potential significance of this assertion for the diagnosis of decision-making deficits, few studies have addressed the influence of GLF on IGT performances in clinical populations, and there is no study to date that involves patients with prefrontal lobe damage. <i>Method.</i> We tested 17 patients with PFC damage and 17 matched healthy controls with the IGT to analyze influence in choice behavior of both long-term outcomes and GLF. <i>Results.</i> There was a difference between groups in the GLF score, but none between groups in the long-term outcome variable (the traditional measure). Our findings demonstrate that only control subjects seemed able to consider both long-term outcome and GLF. <i>Conclusions.</i> The discussion focuses on the contribution of empirical data, which may have implications for the clinical assessment of decision-making ability with the IGT.
DOI: 10.6084/m9.figshare.1579442.v1
title: Data & materials for Moutsiana et al (unpublished)

description: This archive contains stimulus presentation and analysis code as well as the data from behavioural experiments in our study 'Cortical idiosyncrasies predict the perception of object size' by Moutsiana et al. (currently unpublished). Processed pRF data from the neuroimaging experiments are available on Zenodo.