cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/99tbnvjhsh.1
title: A transcriptome assembly and its annotation for Citrus aurantifolia leaves

description: Mexican lime (Citrus aurantifolia) is an important economic crop in tropical and sub-tropical areas including the Pacific region of Mexico. Nowadays, is seriously affected by Huanglongbing (HLB) disease, associated to Candidatus Liberibacter asiaticus (CLas). Transcriptomic profile approaches represent the first step to understand the molecular mechanisms involved in the pathogenic process. To date, reference genomes of Citrus sinensis and Citrus clementina is being used for transcriptomic studies in citrus since a reference transcriptome for acid limes including Mexican lime is not available. In the present study, a Citrus aurantifolia de novo transcriptome was generated from leaves tissue including four conditions: asymptomatic CLas-infected plants (early stage of HLB disease, 8 weeks post inoculation, wpi), symptomatic CLas-infected plants (late stage of HLB disease, 16 wpi) and mock-inoculated control plants at both time points, 8 and 16 wpi. Pools of equimolar quantities of total RNA from 5 plants for each experimental condition, were used for cDNA synthesis and construction of a total of four libraries. Hight-throughput sequencing was performed in Illumina NexSeq500 platform, and assembled transcriptome was constructed using Oases (v.0.2.01). After filtering and removal of redundant sequences, 41,600 tentative transcripts (TTs) were produced with a mean length of 1,838 bp, of which 86.13% were over 500 bp in length, N50 of 2,415 bp and full transcriptome length of 76.60 MB. A total of 34,123 (82.18%) TTs had a confident orthologue, 26,614 TTs encoded complete proteins, and 16,426 were non-redundant according to their TAIR10 and UniProtKB identifier (ID). Annotation also revealed that 6,994 of TTs had no significant homology to any other plant gene, even though 1,438 TTs were predicted to code for complete. In the present data set, a complete transcript annotation in excel format, and full-assembled transcriptome in fasta format are provided. This data is the first hybrid transcriptome of Citrus aurantifolia from both healthy and CLas-infected leaves tissue. The de novo assembled transcriptome represents a valuable reference tool for differential expression analysis for Mexican lime and other acid limes in both healthy and pathogen-challenge conditions. Additionally, the data could be useful for citrus breeding programs and designing of novel diagnostic tools.
DOI: 10.25919/5dbc66749a1e8
title: Parkes observations for project P958 semester 2019OCTS_11

description: Fast radio bursts (FRBs) continue to raise more questions than they answer. Until last year, only one burst – the only one known to repeat - had been localized to a bright radio nebula (either a young supernova remnant or pulsar wind nebulae) in a distant dwarf galaxy. Over the last two year searches with the Australian Square Kilometre Array Pathfinder (ASKAP) have detected 31 bursts, five of which have been localised to host galaxies at redshifts ranging from 0.1 to 0.5. These bursts and their hosts are very unlike the repeater, suggesting there may be a dichotomy in the population. However one of the arcminute-localised ASKAP FRBs has recently been found to repeat. Here we propose to search and study repetitions in this FRB population. Our comprehensive sample and a dense monitoring campaign of well localised bursts, at a fluence limit more than 60 times lower than that of their detections to characterise the fraction of bursts that repeat. For bursts that repeat the unique wide bandwidth observations will be used to test leading models of burst emission.
DOI: 10.17632/9c68wk6jcy.1
title: FAST TRACK GUIDES

description: It contains several tips of methodology, papers structure and... Has a form of fast track guide.
DOI: 10.17632/sfwkmvmmd5.1
title: EEG data (from real-time neurofeedback experiment)

description: EEG_epochs_sample.npy: numPy array of size [1200, 550, 32] corresponding to [trials, samples, channels]. The data is recorded with a sampling frequency of 500Hz using Enobio 32 (Neuroelectrics), i.e. 1100 ms of data (100 ms pre-stimulus onset, 1000 ms post-stimulus onset). The channels are ordered as: ['P7', 'P4', 'Cz', 'Pz', 'P3', 'P8', 'O1', 'O2', 'T8', 'F8', 'C4', 'F4', 'Fp2', 'Fz', 'C3', 'F3', 'Fp1', 'T7', 'F7', 'Oz', 'PO3', 'AF3', 'FC5', 'FC1', 'CP5', 'CP1', 'CP2', 'CP6', 'AF4', 'FC2', 'FC6', 'PO4']. y_categories_sample.npy: Contains binary category labels for each (visual) trial. 0 corresponds to a "scene" category. 1 corresponds to a "face" category. More information here: https://github.com/gretatuckute/ClosedLoop/blob/master/README.md
DOI: 10.5281/zenodo.3524866
title: Local Voting Z: Source code and datasets.

description: DataSet with results and code for paper submitted to Computer Networks
DOI: 10.5281/zenodo.3524867
title: Local Voting Z: Source code and datasets.

description: DataSet with results and code for paper submitted to Computer Networks
DOI: 10.17632/ctjfr72bpm.1
title: Protein interaction energy landscapes are shaped by functional and also non-functional partners

description: In the crowded cell, the competition between functional and non-functional interactions is severe. Understanding how a protein binds the right piece in the right way in this complex jigsaw puzzle is crucial and very difficult to address experimentally. To interrogate how this competition constrains the behavior of proteins with respect to their partners or random encounters, we (i) performed thousands of cross-docking simulations to systematically characterize the interaction energy landscapes of functional and non-functional protein pairs and (ii) developed an original theoretical framework based on two-dimensional energy maps that reflect the propensity of a protein surface to interact. Strikingly, we show that the interaction propensity of not only binding sites but also of the rest of protein surfaces is conserved for homologous partners be they functional or not. We show that exploring non-functional interactions (i.e. non-functional assemblies and interactions with non-functional partners) is a viable route to investigate the mechanisms underlying protein-protein interactions. Precisely, our 2D energy maps based strategy enables it in an efficient and automated way. Moreover, our theoretical framework opens the way for the developments of a variety of applications covering functional characterization, binding site prediction, or characterization of protein behaviors in a specific environment. Here, the dataset contains all data produced and analyzed in Schweke, Mucchielli, Sacquin-Mora, Bei and Lopes, Protein interaction energy landscapes are shaped by functional and also non-functional partners. This includes 103x103 protein docking calculations, the resulting 2D energy maps (text and pdf files) and the protein surface properties of the 103 proteins of the study projected in 2D (text and pdf files).
DOI: 10.7910/dvn/ulxrht/cnmqxb
title: Tables 1-2 & A4.do

description: :unav
DOI: 10.7910/dvn/ulxrht/dvk1gf
title: Figure 3.do

description: :unav
DOI: 10.7910/dvn/ulxrht/ktezch
title: Tables 3-4.do

description: :unav
DOI: 10.7910/dvn/ulxrht/pwuhfp
title: Table 5 & OA10.do

description: :unav
DOI: 10.7910/dvn/ulxrht/urb4dk
title: Dataset_2.tab

description: :unav
DOI: 10.7910/dvn/ulxrht/xgfxov
title: Table OA4.do

description: :unav
DOI: 10.17632/7v2vcc9v28.1
title: Evoked intracranial potentials in patients with epilepsy

description: The parameters affecting the evoked response in the brain as a result of brain stimulation is not well understood. Yet it is widely used in research and clinical settings (e.g. responsive neurostimulation to treat intractable multifocal epilepsy in humans). In an effort to better understand the parameters that affect the response to brain stimulation, single pulse electrical stimulation was delivered to different brain regions of patients with epilepsy undergoing long term monitoring. These data were recorded off depth and surface cortical electrodes. These are the summarized trial data derived from patients. 11 patients are included in this data set. The data are organized into a MATLAB variable type table and saved in .mat form. These data were recorded, epoched, filtered, and processed as described in the submitted manuscript "A systematic exploration of parameters affecting evoked intracranial potentials in patients with epilepsy" by authors Bornali Kundu, Tyler S. Davis, Brian Philip, Elliot H. Smith, Amir Arain, Angela Peters, Blake Newman, Christopher R. Butson and John D. Rolston. The columns of the table consistent of the following variables: (1) patientnum - the patient ID number (2) stimlevel - the stimulation level delivered, in microvolts (3) stimchan - the number ID of the stimulation channel (4) respchan - the number ID of the response channel from which the evoked response was measured (5) isdpth - 1 = the channel was from a depth electrode, 0 = the channel was from a cortical surface electrode (6) distance - distance between the stimulation channel and response channel in Euclidian space, in mm (7) issozstim - 1= the stimulation channel was located in the clinical SOZ, boolean variable (8) issozrep - 1= the response channel was located in the clinical SOZ, boolean variable (9) posthgpwr100 - raw trial power after bandpass filtering the epoched data from 70-150Hz, calculating the Hilbert transform of the data, and then calculating the mean from 5 - 100ms as described in the methods section, data are log transformed (10) postrawmav100 - raw voltage data mean from 5-100 ms for the trial, in milivolts, data are log transformed (11) trials - trial number ID (12) regionstim - the region of the stimulation channel determined from an atlas as described in the methods (13) regionresp - the region of the response channel determined from an atlas as described in the methods (14) issoz - boolean variable, true corresponds to if the stimulation channel, response channel, or both were in the clinical SOZ (15) regionresptype - categorical description of the region of the response channel (16) regionstimtype - categorical description of the region of the stimulation channel Funding: JDR is supported by the NIH, NCATS KL2 TR002539and NINDS R21 NS113031. BK is supported in part by a NREF neurosurgical research grant.
DOI: 10.17632/kd7krm7ndm.2
title: On the Decomposition of Austenite in a High-Silicon Medium-Carbon Steel During Quenching and Isothermal Holding Above and Below the Martensite Start Temperature

description: These data refer to the paper that submitted to the Journal of Materials characterization.
DOI: 10.17632/wg9shy9rsm.1
title: Finding Faults: a scoping study of Fault Diagnostics for Industrial Cyber-Physical Systems

description: As Industrial Cyber-Physical Systems (ICPS) become more connected and widely-distributed, often operating in safety-critical environments, we require innovative approaches to detect and diagnose the faults that occur in them. We profile fault identification and diagnosis techniques employed in the aerospace, automotive and industrial control domains. Each of these sectors have adopted particular methods to meet their differing fault diagnostic needs. By examining both theoretical presentations as well as case studies from production environments, we present a profile of the current approaches being employed.
DOI: 10.7910/dvn/ulxrht/amolxa
title: Figure 1.do

description: :unav
DOI: 10.7910/dvn/ulxrht/dhyady
title: Table OA5-OA7.do

description: :unav
DOI: 10.7910/dvn/ulxrht/ghlh4p
title: Dataset_Fig_1.tab

description: :unav
DOI: 10.7910/dvn/ulxrht/mprxk4
title: Dataset_1.tab

description: :unav
DOI: 10.7910/dvn/ulxrht/ovhefh
title: Table OA2.do

description: :unav
DOI: 10.7910/dvn/ulxrht/rja0g9
title: Dataset_Fig_3.tab

description: :unav
DOI: 10.7910/dvn/ulxrht/sg7zbw
title: Table OA3.do

description: :unav
DOI: 10.7910/dvn/ulxrht/wbe2fs
title: Table OA8-OA9.do

description: :unav
DOI: 10.15128/r2cv43nw82q
title: Splitting of two-component solitons from collisions with narrow potential barriers [dataset]

description: We consider the interaction of two component bright-bright solitons with a narrow potential barrier (splitter) in the framework of the two-component Gross-Pitaevskii (nonlinear-Schroedinger) system, with self-attraction within each component and cross-attraction between the components, motivated by the splitting of composite solitons facilitating the design of two-component soliton-interferometer schemes. We determine approximate analytic results by assuming a weak potential barrier and applying perturbation theory to the limit where the system becomes integrable. We do this for the case of negligible interspecies interactions, and also when the nonlinearities are strongly asymmetric, such that the wavefunction for the component with a smaller population is solved by neglecting its self-interaction term and the other component constitutes a bright soliton. We use numerical simulations to find the transmissions of both components in regions outside of these approximations and to compare with the approximate analytics, finding that there is an appreciable parameter range where one component is essentially entirely transmitted and the other reflected.
description: Numerical study
DOI: 10.17632/bygfh3hr97.1
title: Data Availability

description: Treated and untreated data from a paper called "Design of a red-emitter hybrid material for bioimaging: europium complexes grafted on silica particles" - Materials Today Chemistry
DOI: 10.17632/dv3pz8xcsp.1
title: A dataset of eco-evidence tools to inform early-stage environmental impact assessments of hydropower development

description: This data supports the publication, McManamay et al. (2019) Evidence-based indicator approach to guide preliminary environmental impact assessments of hydropower development. Ecological Indicators. When using this dataset, please cite this work. The datasets described herein provide the foundation for a decision support prototype (DSP) toolkit aimed at assisting stakeholders in determining evidence of which aspects of river ecosystems have been impacted by hydropower. A series of 42 river function indicators [1,2] were used to characterize divergent aspects of river ecosystems while also serving to consolidate the dimensionality of these complex systems into a manageable number of measures. These indicators were developed from a comprehensive literature review of the environmental impacts of hydropower [3] and are associated with six main categories of impacts to river systems: biota and biodiversity, water quality, hydrology, geomorphology, land cover, and river connectivity. The three tools comprising the DSP toolkit and associated data include: 1) Science-Based Questionnaire (SBQ): A series of structured survey-style 140 questions for understanding impacts of dams on river ecosystems were developed through a global literature review. A spreadsheet program was developed to summarize the results of questions into evidence of dam impacts on the 42 ecological indicators. Output is provided in tabular and graphical/chart formats. 2) Environmental Envelope Model (EEM): The EEM is a model to predict the likelihood of hydropower impacting indicators based on a several variables. The intended use of the EEM is for situations of new hydropower development where results of the SBQ are incomplete or highly uncertain. A dataset containing attributes of dams, reservoirs, and geospatial information on environmental concerns were compiled and combined with data on ecological indicators measured at those sites. The data were used to develop models predicting impacts of dams on ecological indicators. A total of 247 envelopes and weighting factors, representing the individual effect of each variable on each ecological indicator, were developed in a spreadsheet program. 3) River Function Linkage Assessment Tool (RFLAT): The purpose of RFLAT is to examine causal relationships amongst indicators. Based on literature review, a node and edge dataset was developed representing causal relationships (“edges”) between ecological indicators (“nodes)”. Bayes theorem was used estimate conditional probabilities of inter-indicator relationships based on the output of the SBQ. Nodes and edges were imported into R programming environment to visualize ecological indicator networks.
DOI: 10.5281/zenodo.3524842
title: Supporting data for "Spatial Noise Correlations in a Si/SiGe Two-Qubit Device from Bell State Coherences"

description: Datasets, analysis scripts and simulations for "Spatial Noise Correlations in a Si/SiGe Two-Qubit Device from Bell State Coherences". For more information and instructions, see READ ME.txt. For questions, contact Jelmer Boter (j.m.boter@tudelft.nl) or Lieven Vandersypen (l.m.k.vandersypen@tudelft.nl).
DOI: 10.5281/zenodo.3525285
title: cdcam

description: This is the example project data which can be run with the python package cdcam, the Cambridge Digital Communications Assessment Model.
DOI: 10.5281/zenodo.3525286
title: cdcam

description: This is the example project data which can be run with the python package cdcam, the Cambridge Digital Communications Assessment Model.
DOI: 10.17632/6pynsy9s4z.1
title: Effects of biomass and environmental factors on nitrogen removal performance and community structure of ANAMMOX immobilized filler were compared

description: We used high-throughput sequencing technology to record the changes of bacterial community structure before and after operation. The relative abundance of each microflora in the immobilized filler is provided below.
DOI: 10.17632/cymynmkxmj.2
title: Supplemntary data of single pixel imaging experiment

description: Supplmentary data of the application of single pixel imaging using different hadamard matrix orders.
DOI: 10.17632/ndx8wkrfb5.1
title: Voltage signals of several Acoustic Displacement Meters recorded at the stepped spillway of The University of Queensland
DOI: 10.17632/p9r9wttjkm.2
title: Tara Oceans - Marine Plankton Diversity
DOI: 10.17632/yg3x2pfdkn.1
title: Qilu data

description: Understanding the magnitude, nature, and forcing mechanisms of past abrupt changes in Indian Summer Monsoon (ISM) strength is central to characterizing future manifestations in the face of global climate change, particularly at centennial time scales. Here we summarize a 6200 year record of oxygen isotopes from Lake Qilu in Yunnan Province, China. The lake is sensitive to changes in precipitation-evaporation balance and precipitates calcite, potentially providing insight into past hydroclimate through oxygen isotope analysis. Beginning at 5200 cal years BP, oxygen isotopes shift to higher values, indicative of a period of aridity and lower lake levels which persist until 3600 cal years BP. Thereafter, lake levels are extraordinarily stable until 1500 cal years BP. At 1500 cal years BP, measurable anthropogenic impacts occur resulting in the delivery of red, iron-rich catchment soil to the lake and higher oxygen isotope values. These changes are likely the result of land clearance for the expansion of agricultural activities. The Qilu record is remarkably consistent with the record from Xingyun Lake, 10 km to the north, strongly suggesting that regional climate drivers are responsible for the changes after 5200 cal years BP and then the stability from 3600-1500 cal years BP. Comparison of both these records with Dongge Cave illustrate the importance of evaporative enrichment in driving higher oxygen isotope values from 5200 to 3600 cal years BP.
DOI: 10.5281/zenodo.3524944
title: Standardized psychological experiments of the ECHOES project

description: Standardized psychological experiments of the ECHOES project were conducted in six European countries: Bulgaria, Finland, Germany, Italy, Norway and Turkey. The dataset contains raw data in four different formats: dta, rdata, sav and xlsx. Survey questionnaires and data preparation syntax are included.
description: For inquiries, please contact the authors.
DOI: 10.5281/zenodo.3524945
title: Standardized psychological experiments of the ECHOES project

description: Standardized psychological experiments of the ECHOES project were conducted in six European countries: Bulgaria, Finland, Germany, Italy, Norway and Turkey. The dataset contains raw data in four different formats: dta, rdata, sav and xlsx. Survey questionnaires and data preparation syntax are included.
description: For inquiries, please contact the authors.
DOI: 10.5519/qd.4uciwedq
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.18112/openneuro.ds002299.v1.0.0
title: rewardBeast
DOI: 10.7295/w9cil50663
title: CIL:50663, rat, cortical primary neurons
DOI: 10.5281/zenodo.3525287
title: weecology/portalPredictions 2019-11-01

description: Using various models to forecast abundances at Portal
DOI: 10.5281/zenodo.3525288
title: weecology/forecasts 2019-11-01

description: Archived forecasts for future analysis
DOI: 10.5519/qd.9tvjoy50
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (160 records)
DOI: 10.5066/p9p7t6z6
title: Foothill yellow-legged frog (Rana boylii) surveys in Oregon 2019

description: We used visual surveys and environmental DNA (eDNA) sampling to document the presence of all life stages of foothill yellow-legged frogs (Rana boylii) at historically occupied sites. We visited 52 stream reaches (sites) on federal and private lands between June and September of 2019. This dataset includes counts of amphibians, crayfish, and fish observed during each site survey, as well as habitat and water sampling covariates.
DOI: 10.5281/zenodo.3525339
title: Data for: Whole genome phylogeny of Gallus: Introgression and data-type effects

description: Multiple sequence alignments and gene trees from the manuscript "Whole genome phylogeny of Gallus: Introgression and data-type effects." The zip file contains a single folder with a README file that provides details the contents and formats of the files that are included.
DOI: 10.5281/zenodo.3525340
title: Data for: Whole genome phylogeny of Gallus: Introgression and data-type effects

description: Multiple sequence alignments and gene trees from the manuscript "Whole genome phylogeny of Gallus: Introgression and data-type effects." The zip file contains a single folder with a README file that provides details the contents and formats of the files that are included.
DOI: 10.6080/k07h1gss
title: In vivo whole-cell recordings to complex sounds in the mouse auditory cortex
title: CRCNS.org ac-5

description: This dataset is not yet available but is expected to be available before the end of 2019.
DOI: 10.25345/c5qt09
title: MassIVE MSV000084524 - Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440
title: Lignin modifications and the exoproteome of three aromatic catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MSGF+ and abundances inferred using PNNL's DMS and MTS Processing pipeline
DOI: 10.26300/b6za-nt53
title: Supplementary data from publication "Calcium oscillations provide a molecular signature for barriers to interspecific hybridization"
DOI: 10.7910/dvn/zv0owu/0ojplz
title: multi-un-1.tab

description: :unav
DOI: 10.7910/dvn/zv0owu/6zur8s
title: replication.do

description: :unav
DOI: 10.7910/dvn/zv0owu/p6qytf
title: lsa.tab

description: :unav
DOI: 10.7910/dvn/zv0owu/zac2yj
title: lsa-1.tab

description: :unav
DOI: 10.7910/dvn/zv0owu/2pcqi1
title: multi-un.tab

description: :unav