cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29244593
title: Appendix A

description: This file contains a processed sample of simulated data and the results from their analysis.The structure of the contents is described below.<br>1. SimulationsFor each functional group, the dataset includes 5 simulations per simulation scenario.Included in the section "simulated_parameters_real_values":- Nitd: Total number of daily roadkills at site i, month t, day d.- NitD: Total number of roadkills during the maximum number of days a carcass remains visible in the survey area at site i and month t.- NtD: Total number of roadkills across all survey sites combined in month t.<br>Additionally, this section includes the true probability values of detection biases:- pL: Carcass location bias- pP: Carcass persistence bias- pOwalking: Carcass observation bias for walking surveys- pOcycling: Carcass observation bias for cycling surveys- pOdriving: Carcass observation bias for driving surveys<br>2. Bayesian Parameter EstimationIncluded in the section "Bayesian_parameter_estimation":- Posterior estimates for the following parameters: - totalN (NtD): Estimated total number of roadkills - pL - pP - pOwalking - pOcycling - pOdriving<br>Each parameter includes:- Posterior mean- R̂ (R-hat) convergence diagnostic- Full posterior distribution<br><br>
DOI: 10.6084/m9.figshare.29244593.v1
title: Appendix A

description: This file contains a processed sample of simulated data and the results from their analysis.The structure of the contents is described below.<br>1. SimulationsFor each functional group, the dataset includes 5 simulations per simulation scenario.Included in the section "simulated_parameters_real_values":- Nitd: Total number of daily roadkills at site i, month t, day d.- NitD: Total number of roadkills during the maximum number of days a carcass remains visible in the survey area at site i and month t.- NtD: Total number of roadkills across all survey sites combined in month t.<br>Additionally, this section includes the true probability values of detection biases:- pL: Carcass location bias- pP: Carcass persistence bias- pOwalking: Carcass observation bias for walking surveys- pOcycling: Carcass observation bias for cycling surveys- pOdriving: Carcass observation bias for driving surveys<br>2. Bayesian Parameter EstimationIncluded in the section "Bayesian_parameter_estimation":- Posterior estimates for the following parameters: - totalN (NtD): Estimated total number of roadkills - pL - pP - pOwalking - pOcycling - pOdriving<br>Each parameter includes:- Posterior mean- R̂ (R-hat) convergence diagnostic- Full posterior distribution<br><br>
DOI: 10.15468/dl.dckdqm
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macrocarpaea inesiae J.R.Grant & Trunz"
 ]
}

 The dataset includes 9 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021642-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/25hsr638kg
title: 3D photogrammetry-based digital avatars (AVATARGET; PI: M Briguglio)

description: Raw data of the study investigating the reliability and agreement of measurements derived from a three-dimensional digital avatar generated by photogrammetry compared to manual collection. The dataset was used to write the article "Anthropometric Measurements from a 3D Photogrammetry-Based Digital Avatar: A Non-Experimental Cross-Sectional Study to Assess Reliability and Agreement", which was published by the journal Applied Sciences in 2025.
DOI: 10.17632/25hsr638kg.1
title: 3D photogrammetry-based digital avatars (AVATARGET; PI: M Briguglio)

description: Raw data of the study investigating the reliability and agreement of measurements derived from a three-dimensional digital avatar generated by photogrammetry compared to manual collection. The dataset was used to write the article "Anthropometric Measurements from a 3D Photogrammetry-Based Digital Avatar: A Non-Experimental Cross-Sectional Study to Assess Reliability and Agreement", which was published by the journal Applied Sciences in 2025.
DOI: 10.17632/fg6k99k3gx
title: Land use change

description: Surface soil samples (0-10 cm) were taken from three diffenrent land use types; grassland, cropland, and bare fallow. In each of the four field replicates, five-point sampling method was used to collected a composite soil sample. Soil sample was air-dried for 1 week, passing through a 2 mm sieve. A portion of the soil samples was used for initial physicochemical analysis, while the remaining portion was stored for incubation experiments.
DOI: 10.17632/fg6k99k3gx.1
title: Land use change

description: Surface soil samples (0-10 cm) were taken from three diffenrent land use types; grassland, cropland, and bare fallow. In each of the four field replicates, five-point sampling method was used to collected a composite soil sample. Soil sample was air-dried for 1 week, passing through a 2 mm sieve. A portion of the soil samples was used for initial physicochemical analysis, while the remaining portion was stored for incubation experiments.
DOI: 10.17632/m78w6r33hm.1
title: Multicohort oral microbial analysis contributes to non-invasive diagnosis for patients reinfected with SARS-CoV-2 omicron variants

description: Infection with SARS-CoV-2 can lead to alterations in human oral microbiome. Recently, there was a wave of patients reinfected with SARS-CoV-2 omicron variant (ORs) in China. Alterations in the oral microbiome in ORs were still unknown. A total of 2046 participants were enrolled and provided tongue-coating samples, and 1637 samples were ultimately used for sequencing and analysis, including 702 ORs, 184 omicron variant primary-infected patients, 50 wild-type strain primary-infected patients (WTPs), 154 common cold patients and 547 heathy controls (HCs). The results showed that no significant difference in the α diversity of the oral microbiome between the OR and HC groups. Compared with HCs, increased abundance of 13 genera, including Prevotella and Veillonella, and decreased abundance of 12 genera, including Neisseria and Actinomyces, were observed in ORs. Then, 5 OTUs were identified to construct a diagnostic model. In the discovery phase, the training set and test set obtained AUC values of 97.25% and 97.07%. Importantly, the independent validation phase achieved 89.61%. Strikingly, two cross-regional validation phases showed 70.90% and 73.97%. In addition, 92.34%, 95.46 and 85.10% were identified in three cross-disease validation phases. Furthermore, we found although SARS-CoV-2 continued to mutate, the overall composition of the oral microbiome changed little. Among them, the microbial community of WTPs was most disturbed, while that of ORs was least disturbed. This study is the first to characterize the oral microbiome of ORs. A diagnostic model which achieved cross-region and cross-disease validation for ORs may help the diagnosis of OR. 
 The data uploaded include the original clinical data of the participants of this study (Table S1) and the data generated during the analysis process and placed in the supplementary materials of the paper (Table S2-24).
 Please find the title in the first row of each sheet.
DOI: 10.17632/m78w6r33hm
title: Multicohort oral microbial analysis contributes to non-invasive diagnosis for patients reinfected with SARS-CoV-2 omicron variants

description: Following SARS-CoV-2 infection, shifts in the composition of the human oral microbiome have been documented. The status of the oral microbiome in this specific patient group remained unexplored. This study enrolled 2046 participants who provided tongue-coating samples, with 1637 samples (comprising 702 ORs, 184 Omicron-naïve patients, 50 wild-type strain primary infections (WTPs), 154 common cold patients, and 547 healthy controls (HCs)) subjected to sequencing and analysis. 
 The data uploaded include the original clinical data of the participants of this study (Table S1) and the data generated during the analysis process and placed in the supplementary materials of the paper (Table S2-24).
 Please find the title in the first row of each sheet.
DOI: 10.17632/m78w6r33hm.2
title: Multicohort oral microbial analysis contributes to non-invasive diagnosis for patients reinfected with SARS-CoV-2 omicron variants

description: Following SARS-CoV-2 infection, shifts in the composition of the human oral microbiome have been documented. The status of the oral microbiome in this specific patient group remained unexplored. This study enrolled 2046 participants who provided tongue-coating samples, with 1637 samples (comprising 702 ORs, 184 Omicron-naïve patients, 50 wild-type strain primary infections (WTPs), 154 common cold patients, and 547 healthy controls (HCs)) subjected to sequencing and analysis. 
 The data uploaded include the original clinical data of the participants of this study (Table S1) and the data generated during the analysis process and placed in the supplementary materials of the paper (Table S2-24).
 Please find the title in the first row of each sheet.
DOI: 10.17632/rhwh8c758k.1
title: Suppression of Trem2 Expression in Decidual Macrophages by Toxoplasma gondii Tachyzoite Infection and Its Impact on Adverse Pregnancy Outcomes: The Regulatory Role of ATF3.

description: Suppression of Trem2 Expression in Decidual Macrophages by Toxoplasma gondii Tachyzoite Infection and Its Impact on Adverse Pregnancy Outcomes: The Regulatory Role of ATF3.
DOI: 10.17632/rhwh8c758k.2
title: Suppression of Trem2 Expression in Decidual Macrophages by Toxoplasma gondii Tachyzoite Infection and Its Impact on Adverse Pregnancy Outcomes: The Regulatory Role of ATF3.

description: Suppression of Trem2 Expression in Decidual Macrophages by Toxoplasma gondii Tachyzoite Infection and Its Impact on Adverse Pregnancy Outcomes: The Regulatory Role of ATF3.
DOI: 10.17632/rhwh8c758k
title: Suppression of Trem2 Expression in Decidual Macrophages by Toxoplasma gondii Tachyzoite Infection and Its Impact on Adverse Pregnancy Outcomes: The Regulatory Role of ATF3.

description: Suppression of Trem2 Expression in Decidual Macrophages by Toxoplasma gondii Tachyzoite Infection and Its Impact on Adverse Pregnancy Outcomes: The Regulatory Role of ATF3.
DOI: 10.17632/rhwh8c758k.3
title: Suppression of Trem2 Expression in Decidual Macrophages by Toxoplasma gondii Tachyzoite Infection and Its Impact on Adverse Pregnancy Outcomes: The Regulatory Role of ATF3.

description: Suppression of Trem2 Expression in Decidual Macrophages by Toxoplasma gondii Tachyzoite Infection and Its Impact on Adverse Pregnancy Outcomes: The Regulatory Role of ATF3.
DOI: 10.17632/5s5b9mjwbh.1
title: Dataset of Mathematical Terminology and words with POS tags

description: As part of the study, a dataset of mathematical words, phrases and terminology in the Uzbek language was formed.
1) This dataset contains 858 unique words and terms in mathematics.
2) A distinctive feature of the dataset is that the words and terms in it have a weighting coefficient for each of the five mathematical areas (Discrete Mathematics, Geometry, Probability Theory, Differential Equations, Higher Mathematics).
3) The penultimate column of the dataset contains the English translation of this word.
4) The last column of the dataset contains information on the part of speech to which this word belongs.
DOI: 10.15468/dl.m4ykjf
title: Occurrence Download

description: A dataset containing 21618 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'CY'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence."year" &gt;= 2000 AND occurrence."year" &lt;= 2025)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 21618 records were derived from 227 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021636-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/5s5b9mjwbh
title: Dataset of Mathematical Terminology and words with POS tags

description: As part of the study, a dataset of mathematical words, phrases and terminology in the Uzbek language was formed.
1) This dataset contains 858 unique words and terms in mathematics.
2) A distinctive feature of the dataset is that the words and terms in it have a weighting coefficient for each of the five mathematical areas (Discrete Mathematics, Geometry, Probability Theory, Differential Equations, Higher Mathematics).
3) The penultimate column of the dataset contains the English translation of this word.
4) The last column of the dataset contains information on the part of speech to which this word belongs.
DOI: 10.17632/5s5b9mjwbh.2
title: Dataset of Mathematical Terminology and words with POS tags

description: As part of the study, a dataset of mathematical words, phrases and terminology in the Uzbek language was formed.
1) This dataset contains 858 unique words and terms in mathematics.
2) A distinctive feature of the dataset is that the words and terms in it have a weighting coefficient for each of the five mathematical areas (Discrete Mathematics, Geometry, Probability Theory, Differential Equations, Higher Mathematics).
3) The penultimate column of the dataset contains the English translation of this word.
4) The last column of the dataset contains information on the part of speech to which this word belongs.
DOI: 10.15468/dl.edhqp9
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "GadmGid is IND.35_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Potentilla L."
 ]
}

 The dataset includes 92 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021643-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mu5bdr
title: Occurrence Download

description: A dataset containing 303 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Astragalus sinicus L.",
 "Year 1970-2025"
 ]
}

 The dataset includes 303 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021645-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/fv84ndv3kb.1
title: Lysinibacillus macroides 38352 Isolated from Traditional Chinese Fermented Foods: A Dual Effect on Ochratoxin A Detoxification and Immune Suppression Alleviation

description: Ochratoxin A (OTA), a nephrotoxic, immunosuppressive, and potentially carcinogenic mycotoxin produced by Aspergillus and Penicillium species, poses a persistent threat to global food safety and livestock health. In this study, we isolated three OTA-degrading bacterial strains from 28 types of traditional Chinese fermented foods. Among them, Lysinibacillus macroides 38352 exhibited the highest degradation efficiency, removing 51.4% of 2.5 μg/mL OTA within 72 hours at 37 °C, with further increases observed over time. Mechanistic analysis revealed that the degradation was mediated not by cell surface adsorption but by secreted metabolites generated through active cellular metabolism. The strain also demonstrated excellent probiotic properties, including tolerance to pH 2–12 and 0.2% bile salts, sensitivity to 15 antibiotics (indicating no resistance), and no pathogenicity in mice. Notably, oral administration of L. macroides 38352 significantly reversed OTA-induced immunosuppression, enhancing vaccine-induced specific IgG, neutralizing antibody titers, and cytokine levels (IL-1β, IL-4, IL-12, IL-17, and IFN-γ), while also reducing inflammatory damage and improving growth performance in OTA-exposed broilers. 
Figure 1. Isolation of the OTA-degrading strains. (A) Colony and cell morphology of 38351, 38352 and 38362. (B) Removal ratio of OTA by strains.
Figure 2. Phylogenetic tree of the isolated 38351, 38352 and 38362 and related taxa. (A) Phylogenetic Tree Analysis of Isolates Based on Partial 16S rRNA Gene Sequences. (B) Phylogenetic Tree Analysis of Isolates Based on Partial gyrB Gene Sequences.
Figure 3. Degradation properties of OTA by isolated strains. (A) Growth Curve of Isolated Strain 38352 (B) Degradation rate of OTA by different cell components. OTA Degradation Ability of Strain 38352: Effect of Culture Temperature (C), Effect of Different Cell Concentrations (D), and Effect of Culture Time (E).
Figure 4. Results of body weight change monitoring. (A) Line chart of body weight change before poison attack. (B) Histogram of Body Weight Change after Poisoning.
Figure 5. The level of the specific IgG antibody. (A) Specific IgG antibody level in chicken serum before virus attack. (B) Specific IgG antibody level in serum of broilers after 7 days of virus attack.
Figure 6. Gene transcription of immune related cytokines in jejunum (A) and cecal tonsil (B). Data were presented as means ± SD (*P &lt; 0.05, and **P &lt; 0.01).
Table 1. Drug abbreviations: FFC Florfenicol (30 µg), CZO Cefazoline (30 µg), SH Spectinomycin (100 µg), MNO Minocycline (30 µg), TGC Tigecycline (15 µg), MID Midecamycin (30 µg), LZD Linezolid (30 µg), DOX Doxycycline (30 µg), SM streptomycin (10 µg), DA clindamycin (2 µg), AMP Ampicillin (10 µg), VAN Vancomycin (30 µg), AMX Amoxicillin (20 µg), TOB Tobramycin (10 µg), CIP Ciprofloxacin (5 µg), RFP Rifampicin (5 µg), OX Oxacillin (5 µg), NAL Nalidixic acid (30 µg), FOT Fosfomycin (30 µg), TLC ticarcillin (85 µg)
DOI: 10.17632/fv84ndv3kb.2
title: Lysinibacillus macroides 38352 Isolated from Traditional Chinese Fermented Foods: A Dual Effect on Ochratoxin A Detoxification and Immune Suppression Alleviation

description: Ochratoxin A (OTA), a nephrotoxic, immunosuppressive, and potentially carcinogenic mycotoxin produced by Aspergillus and Penicillium species, poses a persistent threat to global food safety and livestock health. In this study, we isolated three OTA-degrading bacterial strains from 28 types of traditional Chinese fermented foods. Among them, Lysinibacillus macroides 38352 exhibited the highest degradation efficiency, removing 51.4% of 2.5 μg/mL OTA within 72 hours at 37 °C, with further increases observed over time. Mechanistic analysis revealed that the degradation was mediated not by cell surface adsorption but by secreted metabolites generated through active cellular metabolism. The strain also demonstrated excellent probiotic properties, including tolerance to pH 2–12 and 0.2% bile salts, sensitivity to 15 antibiotics (indicating no resistance), and no pathogenicity in mice. Notably, oral administration of L. macroides 38352 significantly reversed OTA-induced immunosuppression, enhancing vaccine-induced specific IgG, neutralizing antibody titers, and cytokine levels (IL-1β, IL-4, IL-12, IL-17, and IFN-γ), while also reducing inflammatory damage and improving growth performance in OTA-exposed broilers. 
Figure 1. Isolation of the OTA-degrading strains. (A) Colony and cell morphology of 38351, 38352 and 38362. (B) Removal ratio of OTA by strains.
Figure 2. Phylogenetic tree of the isolated 38351, 38352 and 38362 and related taxa. (A) Phylogenetic Tree Analysis of Isolates Based on Partial 16S rRNA Gene Sequences. (B) Phylogenetic Tree Analysis of Isolates Based on Partial gyrB Gene Sequences.
Figure 3. Degradation properties of OTA by isolated strains. (A) Growth Curve of Isolated Strain 38352 (B) Degradation rate of OTA by different cell components. OTA Degradation Ability of Strain 38352: Effect of Culture Temperature (C), Effect of Different Cell Concentrations (D), and Effect of Culture Time (E).
Figure 4. Results of body weight change monitoring. (A) Line chart of body weight change before poison attack. (B) Histogram of Body Weight Change after Poisoning.
Figure 5. The level of the specific IgG antibody. (A) Specific IgG antibody level in chicken serum before virus attack. (B) Specific IgG antibody level in serum of broilers after 7 days of virus attack.
Figure 6. Gene transcription of immune related cytokines in jejunum (A) and cecal tonsil (B). Data were presented as means ± SD (*P &lt; 0.05, and **P &lt; 0.01).
Table 1. Drug abbreviations: FFC Florfenicol (30 µg), CZO Cefazoline (30 µg), SH Spectinomycin (100 µg), MNO Minocycline (30 µg), TGC Tigecycline (15 µg), MID Midecamycin (30 µg), LZD Linezolid (30 µg), DOX Doxycycline (30 µg), SM streptomycin (10 µg), DA clindamycin (2 µg), AMP Ampicillin (10 µg), VAN Vancomycin (30 µg), AMX Amoxicillin (20 µg), TOB Tobramycin (10 µg), CIP Ciprofloxacin (5 µg), RFP Rifampicin (5 µg), OX Oxacillin (5 µg), NAL Nalidixic acid (30 µg), FOT Fosfomycin (30 µg), TLC ticarcillin (85 µg)