cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15599285
title: A Conversational Brain-Artificial Intelligence Interface
title: EEGChat

description: Dataset for the paper "A Conversational Brain-Artificial Intelligence Interface". (arXiv: https://arxiv.org/abs/2402.15011)

Five subjects were recorded: subject1, subject2, subject3, subject4, and subject5.

For each subject, the following files are provided:




subjectX.eeg, subjectX.vhdr, subjectX.vmrk
the raw EEG recordings of the experiment


subjectX_info.json, subjectX_trials.json
logs of events throughout the experiment


subjectX_model.keras
the model used during the training of the classifier


subjectX_model_refitted.keras
the classifiers refitted on all data recorded during the training, used  during the experiment to decode cVEP selections


subjectX_train_test_data.zip
a zip, containing the exact windows of data used to train and test the cVEP classifier




To analyze the raw data, information from the logs needs to be integrated, as it contains the selections of the subject.

The following triggers/markers are used in the EEG data:




experiment_start
100


rs_open_start
200


rs_open_end
201


rs_closed_start
210


rs_closed_end
211


calibration_block_start
110


calibration_block_end
111


training_start
120


new_block_train
129


training_end
121


evaluation_start
130


new_block_eval
139


evaluation_end
131


accucary_eval_block_start
140


accucary_eval_block_end
141


experiment_end
101


trial_start
1


rec_audio_start
2


rec_audio_end
3


stim_start
4


stim_end
5


stim_new_rep
6


audio_start
7


audio_end
8


trial_end
9




The most important markers for analysis are stim_start and stim_end, as these denote the start and end of the cVEP flashing.
DOI: 10.5281/zenodo.15599286
title: A Conversational Brain-Artificial Intelligence Interface
title: EEGChat

description: Dataset for the paper "A Conversational Brain-Artificial Intelligence Interface". (arXiv: https://arxiv.org/abs/2402.15011)

Five subjects were recorded: subject1, subject2, subject3, subject4, and subject5.

For each subject, the following files are provided:




subjectX.eeg, subjectX.vhdr, subjectX.vmrk
the raw EEG recordings of the experiment


subjectX_info.json, subjectX_trials.json
logs of events throughout the experiment


subjectX_model.keras
the model used during the training of the classifier


subjectX_model_refitted.keras
the classifiers refitted on all data recorded during the training, used  during the experiment to decode cVEP selections


subjectX_train_test_data.zip
a zip, containing the exact windows of data used to train and test the cVEP classifier




To analyze the raw data, information from the logs needs to be integrated, as it contains the selections of the subject.

The following triggers/markers are used in the EEG data:




experiment_start
100


rs_open_start
200


rs_open_end
201


rs_closed_start
210


rs_closed_end
211


calibration_block_start
110


calibration_block_end
111


training_start
120


new_block_train
129


training_end
121


evaluation_start
130


new_block_eval
139


evaluation_end
131


accucary_eval_block_start
140


accucary_eval_block_end
141


experiment_end
101


trial_start
1


rec_audio_start
2


rec_audio_end
3


stim_start
4


stim_end
5


stim_new_rep
6


audio_start
7


audio_end
8


trial_end
9




The most important markers for analysis are stim_start and stim_end, as these denote the start and end of the cVEP flashing.
DOI: 10.17632/b6gxn3m8vj
title: Supplementary data for "Vegetation and the formation of regolith-hosted REE deposits from granitic rocks: The mercury isotope perspective"

description: Raw data for all figures in the manuscript by Feng et al. to be published by Mineralium Deposita as "Vegetation and the formation of regolith-hosted REE deposits from granitic rocks: The mercury isotope perspective"
DOI: 10.17632/b6gxn3m8vj.1
title: Supplementary data for "Vegetation and the formation of regolith-hosted REE deposits from granitic rocks: The mercury isotope perspective"

description: Raw data for all figures in the manuscript by Feng et al. to be published by Mineralium Deposita as "Vegetation and the formation of regolith-hosted REE deposits from granitic rocks: The mercury isotope perspective"
DOI: 10.17632/xk8jrf7dh8
title: Digital Intelligence Technology Application and Export Resilience dataset

description: This dataset helps to empirically analyze the relationship among the Digital Intelligence Technology Application and export resilience.
DOI: 10.17632/xk8jrf7dh8.1
title: Digital Intelligence Technology Application and Export Resilience dataset

description: This dataset helps to empirically analyze the relationship among the Digital Intelligence Technology Application and export resilience.
DOI: 10.15468/dl.rz87ac
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Xenodermichthys copei (Gill, 1884)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((17.8454 -33.8607,17.8905 -34.1504,17.9648 -34.1504,17.9648 -25.1504,14.3389 -25.1504,14.4725 -26.5137,15.1589 -28.0715,16.3623 -29.3594,16.8947 -30.6715,17.7447 -31.9232,17.8096 -32.2341,17.5192 -32.4186,17.3515 -32.9009,17.8454 -33.8607))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010514-250525065834625/datasets/export for details.
DOI: 10.3886/e231550
title: Replication data for: CONDI: A Cost-of-Nominal-Distortions Index

description: We construct a PCE-based price index whose weights minimize the welfare costs of nominal distortions: a cost-of-nominal-distortions index. We compute these weights in a multi-sector New Keynesian model, calibrated to match US data on price stickiness, labor shares,
and inflation across sectors. The CONDI weights mostly depend on price stickiness. Moreover, CONDI stabilization leads to negligible welfare losses compared to the optimal policy and is better approximated by core rather than headline inflation targeting. An even better approximation can be obtained with an adjusted core index. (JEL C14, E12, E25, E31, E52).
DOI: 10.3886/e231550v1
title: Replication data for: CONDI: A Cost-of-Nominal-Distortions Index

description: We construct a PCE-based price index whose weights minimize the welfare costs of nominal distortions: a cost-of-nominal-distortions index. We compute these weights in a multi-sector New Keynesian model, calibrated to match US data on price stickiness, labor shares,
and inflation across sectors. The CONDI weights mostly depend on price stickiness. Moreover, CONDI stabilization leads to negligible welfare losses compared to the optimal policy and is better approximated by core rather than headline inflation targeting. An even better approximation can be obtained with an adjusted core index. (JEL C14, E12, E25, E31, E52).
DOI: 10.3886/e231551
title: Replication data for: Approximating the Cost-of-Living Index for a Storable Good

description: This paper estimates a cost-of-living index using a dynamic structural model for two storable product categories. In each category, regime shifts to higher or lower retail prices are observed. Fixed-base indexes do a poor job of capturing changes in welfare after a regime shift, and deviate from the dynamic index by as much as 300 percent. I evaluate the extent to which two recently proposed indexes can approximate the model-derived index. These indexes improve welfare measurement and are straightforward to compute. The category's competitive structure and features of the regime shift determine which of the two provides a better approximation.
DOI: 10.3886/e231551v1
title: Replication data for: Approximating the Cost-of-Living Index for a Storable Good

description: This paper estimates a cost-of-living index using a dynamic structural model for two storable product categories. In each category, regime shifts to higher or lower retail prices are observed. Fixed-base indexes do a poor job of capturing changes in welfare after a regime shift, and deviate from the dynamic index by as much as 300 percent. I evaluate the extent to which two recently proposed indexes can approximate the model-derived index. These indexes improve welfare measurement and are straightforward to compute. The category's competitive structure and features of the regime shift determine which of the two provides a better approximation.
DOI: 10.15468/dl.e8an2p
title: Occurrence Download

description: A dataset containing 1147 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((62.5805 -10.6597,181.85075 -10.6597,181.85075 56.21026,62.5805 56.21026,62.5805 -10.6597))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is one of (Geodetic datum assumed WGS84, Coordinate rounded)",
 "TaxonKey is Saururus chinensis"
 ]
}

 The dataset includes 1147 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001206-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g633d
title: Data from: Optimal numbers of matings: the conditional balance between benefits and costs of mating for females of a nuptial gift-giving spider

description: In species where females gain a nutritious nuptial gift during mating, the
 balance between benefits and costs of mating may depend on access to food.
 This means that there is not one optimal number of matings for the female
 but a range of optimal mating numbers. With increasing food availability,
 the optimal number of matings for a female should vary from the number
 necessary only for fertilization of her eggs to the number needed also for
 producing these eggs. In three experimental series, the average number of
 matings for females of the nuptial gift-giving spider Pisaura mirabilis
 before egg sac construction varied from 2 to 16 with food-limited females
 generally accepting more matings than well-fed females. Minimal level of
 optimal mating number for females at satiation feeding conditions was
 predicted to be 2–3; in an experimental test, the median number was 2
 (range 0–4). Multiple mating gave benefits in terms of increased fecundity
 and increased egg hatching success up to the third mating, and it had
 costs in terms of reduced fecundity, reduced egg hatching success after
 the third mating, and lower offspring size. The level of polyandry seems
 to vary with the female optimum, regulated by a satiation-dependent
 resistance to mating, potentially leaving satiated females in lifelong
 virginity.
description: Data from: Optimal
 numbers of matings: the conditional balance between benefits and costs of
 mating for females of a nuptial gift-giving spiderData
 JEB-2014-00530.xlsx
DOI: 10.5281/zenodo.18266590
title: Age dependent priming in Arabidopsis proteomics

description: The data are proteomic files related to Arabidospsis plants, adults and seedling, with four conditions: control, infected with Plectosphaerella cucunerina, treated with indol-3-carboxylic acid, and treated with indol-3-carboxylic acid and infected with the same pathogen.  For SEEDLING plants: 1-2-3 are control plants; 4-5-6 are infected plants; 7-8-9 are treated plants; 10-11-12 are treated infected plants. For ADULT plants: the same conditions 13-14-15 control plants; 16-17-18 control infected plants; 19-20-21 are treated plants and 22-23-24 are treated and infected plants. For more information, check the publication
DOI: 10.5281/zenodo.18266589
title: Age dependent priming in Arabidopsis proteomics

description: The data are proteomic files related to Arabidospsis plants, adults and seedling, with four conditions: control, infected with Plectosphaerella cucunerina, treated with indol-3-carboxylic acid, and treated with indol-3-carboxylic acid and infected with the same pathogen.  For SEEDLING plants: 1-2-3 are control plants; 4-5-6 are infected plants; 7-8-9 are treated plants; 10-11-12 are treated infected plants. For ADULT plants: the same conditions 13-14-15 control plants; 16-17-18 control infected plants; 19-20-21 are treated plants and 22-23-24 are treated and infected plants. For more information, check the publication
DOI: 10.6084/m9.figshare.21629646
title: Complete genome sequencing and comparative genomic analyses of a new spotted-fever <i>Rickettsia heilongjiangensis</i> strain B8

description: <i>Rickettsia heilongjiangensis</i>, a tick-borne obligate intracellular bacterium and causative agent of spotted fever in China, has attracted increasing concern regarding its capability in causing human rickettsiosis. Here, we conducted a genomic analysis of a new <i>R. heilongjiangensis</i> strain B8 (B8) isolated from the serum of a patient who had been bitten by a <i>Haemaphysalis longicornis</i> tick in Anhui Province, China. The present study sought to identify exclusive genes that might be associated with the pathogenicity of B8 using comparative genomics. Specifically, the sequences of B8 were assembled into one circular chromosome of 1,275,081 bp and predicted to contain 1447 genes. Comparative genome analyses were performed based on the genome of B8 and 28 spotted fever group (SFG) rickettsial genomes deposited in NCBI. Phylogenomic analyses indicated the B8 strain was clustered within the <i>R. heilongjiangensis</i> species; however, a sum of 112 and 119 B8-unique genes was identified when compared with <i>R. heilongjiangensis</i> and <i>R. japonica</i> strains, respectively. Functional annotation analyses revealed that these B8-unique genes were mainly annotated to defence mechanisms, lipid transport and metabolism, cell wall/membrane/envelope biogenesis. These data indicate B8 rather represents a previously undescribed human-pathogenic SFG rickettsia lineage, which may be an intermediate lineage of <i>R. heilongjiangensis</i> and <i>R. japonica</i>. Overall, this study isolated a new strain of <i>R. heilongjiangensis</i> in East-Central China for the first time, and provided potential B8-unique genetic loci that could be used for the discrimination of B8 from other R. <i>heilongjiangensis</i> and closely related SFG <i>Rickettsial</i> strains.
DOI: 10.6084/m9.figshare.21629646.v2
title: Complete genome sequencing and comparative genomic analyses of a new spotted-fever <i>Rickettsia heilongjiangensis</i> strain B8

description: <i>Rickettsia heilongjiangensis</i>, a tick-borne obligate intracellular bacterium and causative agent of spotted fever in China, has attracted increasing concern regarding its capability in causing human rickettsiosis. Here, we conducted a genomic analysis of a new <i>R. heilongjiangensis</i> strain B8 (B8) isolated from the serum of a patient who had been bitten by a <i>Haemaphysalis longicornis</i> tick in Anhui Province, China. The present study sought to identify exclusive genes that might be associated with the pathogenicity of B8 using comparative genomics. Specifically, the sequences of B8 were assembled into one circular chromosome of 1,275,081 bp and predicted to contain 1447 genes. Comparative genome analyses were performed based on the genome of B8 and 28 spotted fever group (SFG) rickettsial genomes deposited in NCBI. Phylogenomic analyses indicated the B8 strain was clustered within the <i>R. heilongjiangensis</i> species; however, a sum of 112 and 119 B8-unique genes was identified when compared with <i>R. heilongjiangensis</i> and <i>R. japonica</i> strains, respectively. Functional annotation analyses revealed that these B8-unique genes were mainly annotated to defence mechanisms, lipid transport and metabolism, cell wall/membrane/envelope biogenesis. These data indicate B8 rather represents a previously undescribed human-pathogenic SFG rickettsia lineage, which may be an intermediate lineage of <i>R. heilongjiangensis</i> and <i>R. japonica</i>. Overall, this study isolated a new strain of <i>R. heilongjiangensis</i> in East-Central China for the first time, and provided potential B8-unique genetic loci that could be used for the discrimination of B8 from other R. <i>heilongjiangensis</i> and closely related SFG <i>Rickettsial</i> strains.
DOI: 10.6084/m9.figshare.22817718
title: Mutations in SARS-CoV-2 variant nsp6 enhance type-I interferon antagonism

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve after its emergence. Given its importance in viral infection and vaccine development, mutations in the viral Spike gene have been studied extensively; however, the impact of mutations outside the Spike gene are poorly understood. Here, we report that a triple deletion (ΔSGF or ΔLSG) in nonstructural protein 6 (nsp6) independently acquired in Alpha and Omicron sublineages of SARS-CoV-2 augments nsp6-mediated antagonism of type-I interferon (IFN-I) signaling. Specifically, these triple deletions enhance the ability of mutant nsp6 to suppress phosphorylation of STAT1 and STAT2. A parental SARS-CoV-2 USA-WA1/2020 strain containing the nsp6 ΔSGF deletion (ΔSGF-WA1) shows reduced susceptibility to IFN-I treatment <i>in vitro</i>, outcompetes the parental strain in human primary airway cultures, and increases virulence in mice; however, the ΔSGF-WA1 virus is less virulent than the Alpha variant (which has the nsp6 ΔSGF deletion and additional mutations in other genes). Analyses of host responses from ΔSGF-WA1-infected mice and primary airway cultures reveal activation of pathways indicative of a cytokine storm. These results provide evidence that mutations outside the Spike protein affect virus-host interactions and may alter pathogenesis of SARS-CoV-2 variants in humans.
DOI: 10.6084/m9.figshare.22817718.v1
title: Mutations in SARS-CoV-2 variant nsp6 enhance type-I interferon antagonism

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve after its emergence. Given its importance in viral infection and vaccine development, mutations in the viral Spike gene have been studied extensively; however, the impact of mutations outside the Spike gene are poorly understood. Here, we report that a triple deletion (ΔSGF or ΔLSG) in nonstructural protein 6 (nsp6) independently acquired in Alpha and Omicron sublineages of SARS-CoV-2 augments nsp6-mediated antagonism of type-I interferon (IFN-I) signaling. Specifically, these triple deletions enhance the ability of mutant nsp6 to suppress phosphorylation of STAT1 and STAT2. A parental SARS-CoV-2 USA-WA1/2020 strain containing the nsp6 ΔSGF deletion (ΔSGF-WA1) shows reduced susceptibility to IFN-I treatment <i>in vitro</i>, outcompetes the parental strain in human primary airway cultures, and increases virulence in mice; however, the ΔSGF-WA1 virus is less virulent than the Alpha variant (which has the nsp6 ΔSGF deletion and additional mutations in other genes). Analyses of host responses from ΔSGF-WA1-infected mice and primary airway cultures reveal activation of pathways indicative of a cytokine storm. These results provide evidence that mutations outside the Spike protein affect virus-host interactions and may alter pathogenesis of SARS-CoV-2 variants in humans.
DOI: 10.6084/m9.figshare.22644491
title: Development of an mRNA vaccine against a panel of heterologous H1N1 seasonal influenza viruses using a consensus hemagglutinin sequence

description: Seasonal influenza, causes hundreds of thousands of deaths annually, posing a severe threat to human health. Currently available influenza vaccines are targeted only at specific strains or conserved epitopes; however, these vaccines are not completely efficacious because influenza viruses can undergo mutation during circulation, leading to antigenic mismatch between recommended strains and circulating strains and elusion from the immune system. Therefore, developing an influenza vaccine that is quick, effective, and broadly protective has become crucial, and the integral part of hemagglutinin (HA) remains an ideal target for vaccine development. This study developed a lipid nanoparticle-encapsulated nucleoside-modified mRNA vaccine (mRNA-LNPs) encoding a consensus full-length HA sequence (H1c) and evaluated its protective efficacy and immunogenicity through in vitro and in vivo assays. Following two intramuscular immunizations (2, 10 µg, or 20 µg) at a 3-week interval in BALB/c mice, H1c-mRNA-LNP vaccine induced strong antibodies as shown in the hemagglutination-inhibition test and protective neutralizing antibodies against numerous heterologous H1N1 influenza viruses as shown in the microneutralization assay. Additionally, both Th1- and Th2-biased cellular immune responses were elicited, with the Th1-biased response being stronger. Two doses of the H1c-mRNA-LNP vaccine could neutralize a panel of heterologous H1N1 influenza viruses and could confer protection in mice. Taken together, these findings suggest that the H1c-mRNA-LNP vaccine encoding a consensus full-length HA is a feasible strategy for developing a cross-protective vaccine against a panel of heterologous H1N1 influenza viruses.
DOI: 10.6084/m9.figshare.22644491.v2
title: Development of an mRNA vaccine against a panel of heterologous H1N1 seasonal influenza viruses using a consensus hemagglutinin sequence

description: Seasonal influenza, causes hundreds of thousands of deaths annually, posing a severe threat to human health. Currently available influenza vaccines are targeted only at specific strains or conserved epitopes; however, these vaccines are not completely efficacious because influenza viruses can undergo mutation during circulation, leading to antigenic mismatch between recommended strains and circulating strains and elusion from the immune system. Therefore, developing an influenza vaccine that is quick, effective, and broadly protective has become crucial, and the integral part of hemagglutinin (HA) remains an ideal target for vaccine development. This study developed a lipid nanoparticle-encapsulated nucleoside-modified mRNA vaccine (mRNA-LNPs) encoding a consensus full-length HA sequence (H1c) and evaluated its protective efficacy and immunogenicity through in vitro and in vivo assays. Following two intramuscular immunizations (2, 10 µg, or 20 µg) at a 3-week interval in BALB/c mice, H1c-mRNA-LNP vaccine induced strong antibodies as shown in the hemagglutination-inhibition test and protective neutralizing antibodies against numerous heterologous H1N1 influenza viruses as shown in the microneutralization assay. Additionally, both Th1- and Th2-biased cellular immune responses were elicited, with the Th1-biased response being stronger. Two doses of the H1c-mRNA-LNP vaccine could neutralize a panel of heterologous H1N1 influenza viruses and could confer protection in mice. Taken together, these findings suggest that the H1c-mRNA-LNP vaccine encoding a consensus full-length HA is a feasible strategy for developing a cross-protective vaccine against a panel of heterologous H1N1 influenza viruses.