cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28377143.v1
title: Raw fasta, alignments and trees files used in mito-APG analysis

description: Reconstructing the phylogenetic relationships among the five major angiosperm clades remains a formidable challenge, as large-scale nuclear and plastid datasets often yield inconsistent frameworks. To evaluate the utility of mitochondrial genomes in resolving these relationships, we assembled the first complete mitochondrial genomes for <i>Ceratophyllum</i> and <i>Chloranthus</i>, thereby filling a critical genomic data gap for key lineages. We constructed five mitochondrial datasets (CDS, protein, codon12, C-to-U edited, and C-to-U deleted CDS) along with three plastid datasets (CDS, protein, and codon12) and employed diverse phylogenetic reconstruction methods (concatenation and coalescent approaches) with various models. Our analyses revealed significant topological conflicts between mitochondrial and plastid phylogenies. Specifically, mitochondrial trees consistently supported a sister-group relationship between <i>Ceratophyllum</i> and <i>Chloranthus</i>, and more than half of the mitochondrial datasets resolved eudicots and monocots as sister groups, whereas plastid trees displayed greater consistency. Notably, editing or deleting RNA editing sites from mitochondrial sequences increased tree stability. Widespread gene-tree heterogeneity was observed, with high-conflict genes tending to have lower sequence entropy and shorter lengths—suggesting that insufficient phylogenetic signal, rather than slow evolution rates, is the primary source of conflict.
DOI: 10.6084/m9.figshare.28377143.v2
title: The original FASTA sequences, alignment matrices, and all resulting phylogenetic tree files used in mito-APG analysis

description: Resolving the phylogenetic relationships among the five major angiosperm lineages remains challenging, with large-scale nuclear and plastid datasets often yielding conflicting topologies. We successfully assembled the first complete mitochondrial genomes for two of the five major lineages within core angiosperm—Ceratophyllales (Ceratophyllum) and Chloranthales (Chloranthus)—and comprehensively assessed the utility of mitochondrial genome in resolving deep angiosperm phylogeny. Through analyses of multiple mitochondrial and plastid datasets using diverse phylogenetic methods, we found consistent support for two important relationships despite overall topological discordance between genomic compartments: (1) all mitochondrial datasets recovered Ceratophyllum + Chloranthus as a monophyletic clade with strong support, and (2) protein-based analyses from both mitochondrial and plastid genomes, along with approximately half of all mitochondrial trees, supported monocots and eudicots as sister groups. We demonstrate that topological instability often observed in mitochondrial phylogenies can be effectively mitigated through RNA editing adjustment strategies (C-to-U edit or delete), which significantly increased tree consistency across inference methods. However, substantial gene tree conflict persisted, particularly at deep nodes. Our investigation revealed that this conflict frequency is significantly negatively correlated with gene entropy (R = -0.55, p &lt; 0.01) and sequence length (R = -0.63, p &lt; 0.001), but showed no significant direct correlation with overall evolution rate or informative sites ratio. Based on these findings, we developed a marker optimization framework integrating both the rate of evolution and entropy, identifying five optimal low-conflict markers (atp1, atp4, ccmFC, matR, rps3). Furthermore, differences in mitogenomic architectural features exhibited strong phylogenetic signals (Blomberg’s K), with GC content (K = 0.948, p&lt;0.001) and RNA editing site numbers (K = 1.092, p&lt;0.001) showing significant phylogenetic conservation and independently supporting the monocot-eudicot sister relationship through possession of shared characteristics. We also discovered significant negative correlations between branch length and both GC content and RNA editing site abundance. These findings demonstrate that mitochondrial genomic data, when appropriately analyzed considering RNA editing, gene characteristics like entropy, and complemented with genomic feature-based approaches, offers unique and valuable insights for resolving deep phylogenetic relationships in angiosperms.
DOI: 10.60893/figshare.apl.28250903.v1
title: Supplemental Online Material - "High-efficient spin injection in Co/GeSn with ferromagnetic resonance driven spin pumping"

description: "High-efficient spin injection in Co/GeSn with ferromagnetic resonance driven spin pumping"
DOI: 10.6084/m9.figshare.22637605.v1
title: Data for "Proposal of an algorithm-independent definition of effective contour length (EL) and its impacts on pixel-scale specific catchment area (SCA)"

description: This dataset is used for the paper of "Proposal of an algorithm-independenat definition of effective contour length (EL) and its impacts on pixel-scale specific catchment area (SCA)". Therein, 'ellipsoid.txt', 'inverse ellipsoid.txt' and 'Saddle.txt' record the DEMs discretized from ellipsoid, inverse ellipsoid and saddle, respectively. 'Real-world DEM' records the DEM of the YiLuo River basin with a horizontal resolution of 100m and vertical resolution of 1m
DOI: 10.17028/rd.lboro.14178899.v1
title: Supplementary information files for A monolithic single-chip point-of-care platform for metabolomic prostate cancer detection

description: Supplementary files for article A monolithic single-chip point-of-care platform for metabolomic prostate cancer detection. There is a global unmet need for rapid and cost-effective prognostic and diagnostic tools that can be used at the bedside or in the doctor’s office to reduce the impact of serious disease. Many cancers are diagnosed late, leading to costly treatment and reduced life expectancy. With prostate cancer, the absence of a reliable test has inhibited the adoption of screening programs. We report a microelectronic point-of-care metabolite biomarker measurement platform and use it for prostate cancer detection. The platform, using an array of photodetectors configured to operate with targeted, multiplexed, colorimetric assays confined in monolithically integrated passive microfluidic channels, completes a combined assay of 4 metabolites in a drop of human plasma in under 2 min. A preliminary clinical study using L-amino acids, glutamate, choline, and sarcosine was used to train a cross-validated random forest algorithm. The system demonstrated sensitivity to prostate cancer of 94% with a specificity of 70% and an area under the curve of 0.78. The technology can implement many similar assay panels and hence has the potential to revolutionize low-cost, rapid, point-of-care testing.<br>
DOI: 10.6084/m9.figshare.19130147.v1
title: Dataset 7.csv

description: Measurements of the reflection coefficient angular dependency for an MLM, performed using a laboratory reflectometer (curve with symbols)
DOI: 10.6084/m9.figshare.22720711.v1
title: Supplemental Table S1. Means, standard deviations, and correlation coefficients for cardiorespiratory fitness with summary sleep variables

description: Supplemental material for Cardiorespiratory Fitness and Circadian Rhythms in Adolescents: A Pilot Study.
DOI: 10.6084/m9.figshare.26790310.v1
title: The IproK Ontology: A Unified Approach to Managing Construction Project Information

description: To support construction managers in situational awareness and decision-making across different construction phases, it is essential to have formal, machine-readable, and interpretable knowledge models and tools. The objective is to develop a standardized and structured representation of project planning data, encompassing task, schedule, resource, and cost information, by creating three domain ontologies. These ontologies are critical as they provide vocabularies for translating data from proprietary formats to RDF triples. A prototype system was developed using Protégé, an open-source ontology editor, and Owlready2, a package for ontology-oriented programming in Python, to support data translation, querying, and information reasoning. A use case was applied and analyzed to demonstrate the effectiveness of the proposed exchange mechanism in facilitating machine-interpretable data.
DOI: 10.6084/m9.figshare.5718901.v1
title: Ecology and biotechnological potential of bacterial community from three marine sponges of the coast of Rio de Janeiro, Brazil

description: ABSTRACT Marine sponges has been a large reservoir of microbial diversity, with the presence of many species specific populations as well as producing biologically active compounds, which has attracted great biotechnological interest. In order to verify the influence of the environment in the composition of the bacterial community present in marine sponges and biotechnological potential of bacteria isolated from these organisms, three species of sponges and the waters surrounding them were collected in different beaches of Rio de Janeiro, Brazil. The profile of the bacterial community present in sponges and water was obtained by PCR-DGGE technique and the biotechnological potential of the strains isolated by producing amylase, cellulase, protease and biosurfactants. The results showed that despite the influence of the environment in the composition of the microbial community, studied marine sponges shown to have specific bacterial populations, with some, showing potential in the production of substances of biotechnological applications.
DOI: 10.6084/m9.figshare.27156459.v2
title: Electrooculography Dataset for Objective Spatial Navigation Assessment in Healthy Subjects During the Leiden Navigation Test

description: This study explores eye movement as a marker of cognitive and navigational abilities. An electrooculography (EOG) signal dataset from 27 individuals was collected during the Leiden Navigation Test, assessing spatial navigation skills. The dataset includes horizontal and vertical eye movements and scores from the Mini-Mental State Examination and the Wayfinding Questionnaire, which evaluate cognitive function and spatial perception. Researchers can use this data to study the link between eye movement and spatial cognition.<br><b>To Cite This Dataset:</b><br><b>IEEE Format:</b> M. Zibandehpoor, F. Alizadehziri, A. A. Larki, S. Teymouri, and M. Delrobaei, “Electrooculography dataset for objective spatial navigation assessment in healthy participants,” arXiv preprint arXiv:2411.06811,2024.<b>BiB Format: </b>@article{zibandehpoor2024electrooculography,<br> title={Electrooculography Dataset for Objective Spatial Navigation Assessment in Healthy Participants},<br> author={Zibandehpoor, Mobina and Alizadehziri, Fatemeh and Larki, Arash Abbasi and Teymouri, Sobhan and Delrobaei, Mehdi},<br> journal={arXiv preprint arXiv:2411.06811},<br> year={2024}<br>}
DOI: 10.6084/m9.figshare.27255069.v1
title: 2024-10-04 16-15-30.838305.csv

description: 为共享数据以响应科研透明度的倡导，助力学术共同体的发展，本研究以附录的形式构式搭配分析法使用的原始输入表（input）（附表一）以及运行（run）后的输出结果表（output）（附表二）。
DOI: 10.6084/m9.figshare.28046039.v1
title: Research Data for: Stability vs. Activity in Electrocatalytic Hydrogen Production Using Mononuclear Labile Cu(II) and Ni(II) Complexes

description: Research data for Stability vs. Activity in Electrocatalytic Hydrogen Production Using Mononuclear Labile Cu(II) and Ni(II) Complexes.Ligand:Raw data for ligand synthesis including all NMR, IR . Complexes:Raw data of both complexes C1 and C2 characterisation including Mass spec, IR, Elemental analysis, Cyclic Voltammetry, UV-Vis acid stability test. Electrocatalysis:Raw data files of electrocatalysis testing for both complex C1 and C2. Electrode CharacterisationRaw data of SEM, SEM-EDX from electrode characterisation.
DOI: 10.23641/asha.6170483.v1
title: Combined Aphasia and Apraxia of Speech Treatment (CAAST) (Wambaugh et al., 2014)

description: <b>Purpose </b>This investigation was designed to examine the effects of a newly developed treatment for aphasia and acquired apraxia of speech (AOS). Combined Aphasia and Apraxia of Speech Treatment (CAAST) targets language and speech production simultaneously, with treatment techniques derived from Response Elaboration Training (Kearns, 1985) and Sound Production Treatment (Wambaugh, Kalinyak-Fliszar, West, & Doyle, 1998). The purpose of this study was to determine whether CAAST was associated with positive changes in verbal language and speech production with speakers with aphasia and AOS. <b>Method </b>Four participants with chronic aphasia and AOS received CAAST applied sequentially to sets of pictures in the context of multiple baseline designs. CAAST entailed elaboration of participant-initiated utterances, with sound production training applied as needed to the elaborated productions. The dependent variables were (a) production of correct information units (CIUs; Nicholas & Brookshire, 1993) in response to experimental picture stimuli, (b) percentage of consonants correct in sentence repetition, and (c) speech intelligibility.<b> <br>Results and</b> <b>Conclusions </b>CAAST was associated with increased CIU production in trained and untrained picture sets for all participants. Gains in sound production accuracy and speech intelligibility varied across participants; a modification of CAAST to provide additional speech production treatment may be desirable.
DOI: 10.6084/m9.figshare.12339557.v1
title: RDF Triplestores Evaluation

description: RDF triplestores evaluation for throughput
DOI: 10.6084/m9.figshare.14627907.v1
title: Survey database.xls

description: The database was created by surveying respondents via an online questionnaire, for the purpose of examining users' attitudes about the use of e-scooters.
DOI: 10.6084/m9.figshare.13221290.v1
title: Supplementary Material for: Intralymphatic Administration of <b><i>Metagonimus yokogawai</i></b>-Extracted Protein Attenuates Experimental Murine Allergic Rhinitis Model

description: <b><i>Objectives:</i></b> This study aimed to evaluate potential therapeutic effect of <i>Metagonimus yokogawai</i> on the OVA-induced allergic rhinitis model. <b><i>Methods:</i></b> OVA-sensitized mice were used to assess potential therapeutic effect of the extract protein of <i>M. yokogawai</i> (My-TP). My-TP was administrated via the intralymphatic route to cervical lymph nodes. The frequencies of sneezing or nasal rubbing were recorded. Histopathologic evaluation was performed for eosinophil infiltrations in the tissues of the nasal mucosa and skin. The mRNA relative expressions of the cytokine profiles including Th1, Th2, Th17, and Treg subsets in the nasal mucosa, cervical lymph nodes, and spleen were analyzed by quantitative real-time reverse-transcriptase polymerase chain reaction. The potential underlying mechanism was investigated by examining cytokine profiles including IL-4 and Treg subsets from lymphocytes of the spleen by flow cytometry. <b><i>Results:</i></b> Intralymphatic injection of My-TP reduced allergic symptoms and eosinophil infiltration in the nasal mucosa. My-TP-treated group showed markedly decreased levels of OVA-specific IgE and WBC counts in nasal lavage. My-TP-treated group showed the decreased expression levels of IL-4, while those of IL-10 were increased in both the nasal mucosa. The levels of IFN-γ and IL-17 were also decreased in the nasal mucosa and cervical lymph nodes. The immunological mechanism may involve the downregulation of Th2 response and upregulation of Tregs in the nasal mucosa and cervical lymph nodes. <b><i>Conclusions:</i></b> Our results provide the first evidence of potential therapeutic effect of <i>M. yokogawai</i> in OVA-sensitized allergic rhinitis mice, suggesting that a Treg/Th2 reorganization may play a role in clinical course of allergic rhinitis.
DOI: 10.6084/m9.figshare.23617776.v1
title: <strong>Supplementary Data S6</strong> - PLINK associattion testing

description: Output from association testing of individual missense variants in PLINK for the “kveik” vs “beer” phenotype. Sequence substitution and gene columns have been added from SnpEff annotation.
DOI: 10.6084/m9.figshare.27038431.v1
title: EVALUATION OF THE HISPANIOLAN ENDEMIC <i>GRAFFENRIEDA OTTOSCHULZII</i><i> </i>(MELASTOMATACEAE)

description: The putative Hispaniolan endemic <i>Graffenrieda ottoschulzii</i> (syn. = <i>Miconia ottoschulzii</i>) was evaluated morphologically and phylogenetically. Morphological data clearly place the species within <i>Miconia</i>, as the taxon is missing the dorsal appendage on the connective and capsule fruits of <i>Graffenrieda</i><i> </i>but has the berry fruits of <i>Miconia</i>. Phylogenetically <i>G. ottoschulzii</i> was resolved as sister to the widespread and mostly South American, <i>M. pyrifolia</i>, and we conclude here that the two taxa are conspecific. We provide an updated description of <i>M. pyrifolia</i> and lectotypify the name <i>M. ottoschulzii</i>.We have uploaded two datasets, one that contains 779 species of Miconia for testing the position of Miconia ottoschulzii, and the second, which is a reduced dataset of close relatives of M. ottschulzii. We also include both RAxML trees derived from these data.
DOI: 10.17632/9pbkfg73ts
title: Firms in the coffee sector across countries: Culture and Performance

description: This dataset supports the central argument that national culture significantly influences the performance of coffee firms, given that coffee entrepreneurship constitutes an innovation-driven activity where cultural factors play a critical role. Specifically, the dataset highlights how cultural dimensions shape entrepreneurial outcomes in the coffee sector, with a focus on innovation dynamics. Importantly, it addresses a gap in the literature by incorporating five key national cultural dimensions, including the often-overlooked interaction effects with uncertainty avoidance (UA). By capturing these intercultural influences, the dataset offers a more nuanced understanding of how culture conditions entrepreneurial success in global coffee markets.
DOI: 10.17632/9pbkfg73ts.1
title: Firms in the coffee sector across countries: Culture and Performance

description: This dataset supports the central argument that national culture significantly influences the performance of coffee firms, given that coffee entrepreneurship constitutes an innovation-driven activity where cultural factors play a critical role. Specifically, the dataset highlights how cultural dimensions shape entrepreneurial outcomes in the coffee sector, with a focus on innovation dynamics. Importantly, it addresses a gap in the literature by incorporating five key national cultural dimensions, including the often-overlooked interaction effects with uncertainty avoidance (UA). By capturing these intercultural influences, the dataset offers a more nuanced understanding of how culture conditions entrepreneurial success in global coffee markets.
DOI: 10.6084/m9.figshare.14317717.v1
title: Simultaneous determination and difference evaluation of volatile components generated from ginseng fruit by HS-SPME Coupled with GC-MS according to fruit color

description: Abstract The volatile components of fruits of Panax ginseng C.A. Meyer analyzed to interpret whether fruits color affect volatile components. The volatile components in ginseng fruits cultured with 3 different clolors such as red fruits, yellow fruits and orange fruits were isolated by head-space solid-phase microextraction fiber (polydimethylsiloxane 100 μm) and identified by gas chromatography mass spectrometry (GC-MS). Then, the volatile components compared by principal component analvsis (PCA). As the results, the 23 voltile components were identified from 3 colors samples and consisted mainly of sesquiterpene hydrocarbons. The differences among the different colors of the samples were obvious from the PC1 and PC2 scatter point plot. As the conclusion, The volatile components of ginseng fruits are different from those of ginseng roots. the fruits colors can affect to produce the volatile components of ginseng fruits.
DOI: 10.6084/m9.figshare.18393671.v1
title: XW_data_2017-2019.xls

description: AFT data of PD patients in Xuanwu hospital
DOI: 10.6084/m9.figshare.20488530.v1
title: Human fall-Group1.csv

description: It is the physical human fall vibration data, collected by EPH-V11 vibration sensor.
DOI: 10.6084/m9.figshare.21351487.v1
title: Changing distributions of the cosmopolitan mosquito species <i>Culex quinquefasciatus</i> Say and endemic <i>Cx. pervigilans</i> Bergroth (Diptera: Culicidae) in New Zealand

description: New Zealand has 13 endemic mosquito species, which are predominantly bird-biters, exhibiting low levels of vector competence, and are adapted to their native ecosystems. Anthropogenic land-use change are well-suited to domesticated exotic species that have already established here. While some endemic species, such as <i>Culex pervigilans,</i> can also be found vutilising such environments, there are indications of population decline and displacement. The cosmopolitan <i>Cx. quinquefasciatus</i> has been established in New Zealand for more than 180 years, and was believed to be confined to the warmer, northern regions. However, biosecurity records of obtained specimens collected by the National Mosquito Surveillance Program, at various points of entry (POE) for goods and international travel, suggest an expansion of this range. Changes in the distributions of <i>Cx. quinquefasciatus</i> and <i>Cx. pervigilans</i> over the last fifteen years in New Zealand, are evaluated herein, with the conclusion that <i>Cx. quinquefasciatus</i> is increasing both in distribution and population density over time, and should be considered an invasive species. Evidence of a southward spread is likely a result of anthropogenic environmental changes particularly favourable to <i>Cx. quinquefasciatus.</i> A trend of considerable ecological and public health importance. Similarly clear effects on urban <i>Cx. pervigilans</i> populations were not observed.
DOI: 10.6084/m9.figshare.23315222.v1
title: Fastq Dysplasia Dataset

description: Oral potentially malignant disorders (OPMDs) are a group of conditions that carry a risk of oral squamous cell carcinoma (OSCC) development. The presence and grade of epithelial dysplasia is currently the gold standard in determining the risk of progression to OSCC. Recent studies indicate that periodontal disease–associated pathogenic bacteria may play a role in the transition from healthy mucosa to dysplasia and to OSCC. Although the oral microbiome and its dysbiosis have been implicated in the pathogenesis of oral cancer, the microbial signatures associated with the transition from healthy mucosa to dysplasia to carcinogenesis have not been established. To characterize oral microbial signatures during this transition, we performed 16S sequencing and analysed both oral swab and formalin-fixed, paraffin-embedded tissue (FFPE) samples. We collected oral swabs from healthy mucosa (from healthy patients), normal mucosa adjacent to dysplasia, and low-grade oral dysplasia. We also collected FFPE samples from normal mucosa adjacent to OSCC, plus low grade and high-grade oral dysplasia samples. Our data demonstrate significant differences in the alpha and beta microbial diversities during the transition from health to dysplasia and to OSCC, as well as increased dissimilarities among these transitions. We found that the Proteobacteria phyla abundance increased, concurrent with a progressive decrease in the Firmicutes phyla abundance in the transition from health to disease. Additionally, Fusobacteria tended to increase in the transition from health to carcinogenesis. Moreover, we found in swab samples that the oral microbiome may be altered in areas that appear to be normal, including in mucosa that are histologically normal adjacent to dysplasia. In addition, trends in specific microbiome changes in oral swab samples preceded those in the tissues; signifying early detection opportunities for clinical diagnosis. These findings suggest that features of the oral microbiome can serve as novel biomarkers for OSCC disease progression.