cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.6ebd9z
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Goniosupradens paucidentata (A.Milne-Edwards, 1861)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019775-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uvy36s
title: Occurrence Download

description: A dataset containing 247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-123.31861 36.36767,-121.23281 36.36767,-121.23281 38.28478,-123.31861 38.28478,-123.31861 36.36767))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sebastes atrovirens (Jordan & Gilbert, 1880)",
 "Year 2016-2016"
 ]
}

 The dataset includes 247 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019776-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bxm5cs
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Goniosoma paucidentatum A.Milne-Edwards, 1861"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019777-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25402/fvl.14709666
title: Druggability of Cavity Pockets within SARS-CoV-2 Spike Glycoprotein and Pharmacophore-based Drug Discovery

description: Graphical abstract
 
 Table S1. Chemical
 descriptors of 10 derivatives of Compound 38
 
 Table S2. The neighboring
 amino acid residues of the cavity number 10.
 
 Library. SMILES of 10
 derivatives of Compound 38
 
 
 




Hits. SDF format of 410 hits obtained from
virtual screening
DOI: 10.25402/fvl.14974071
title: Targeting SARS-CoV-2 Nsp15 endoribonuclease: An in silico perspective: Supplementary Data.docx

description: <b>Supplementary Table 1</b><br><br>Binding
 affinity of the drug molecules against SARS-CoV-2 Nsp15.
 
 <b>Supplementary Figure 1</b>. 
 
 The
 redocking of the citrate into Nsp15 (PDB ID: 6W01 chain A). the citrate
 moieties are colored according to the color code at the bottom of the figure.
DOI: 10.25402/fvl.15022776
title: Potential drugs against COVID-19 revealed by Gene Expression Profile, Molecular Docking and Molecular Dynamic Simulation: Supplementary File.pptx

description: Binding
site predictions for each of the 27 drugs against SARS-CoV-2 3CL Main Protease
DOI: 10.25402/fvl.16930861
title: Supplementary information.docx: Classification of coronaviruses. Illustration of how the new names of the variants are causing confusion with names assigned to genera in the family Coronaviridae

description: Classification
 of coronaviruses. Illustration of how the new names of the variants are
 causing confusion with names assigned to genera in the family Coronaviridae
 
 



 
 
 Coronavirus
DOI: 10.25402/fvl.16999417
title: Supplementary Table 5a.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 5a</b>: The list of
 experimentally determined Spike protein epitopes along with their start and
 end positions, as predicted from 8 independent studies.
DOI: 10.25402/fvl.16999423
title: Supplementary Table 1a.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 1a</b>: All frequently
 mutated amino acid residues that have encountered substitutions in 2% or more
 of all SARS-CoV-2 isolates, in at least one country, before May (Group B).
 The frequencies above 2% have been highlighted in ‘red’
DOI: 10.25402/fvl.16999426
title: Supplementary Table 5b.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 5b</b>: The list of
 bioinformatically predicted Spike protein epitopes along with their start and
 end positions, as predicted from 3 independent studies, given in individual
 sheets
DOI: 10.25402/fvl.16999429
title: Supplementary Table 2.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 2</b>: The frequencies per
 100 amino acids for all viral proteins, for all frequently mutated amino acid
 substitutions, calculated individually for each country. The frequencies for
 the two groups (labelled ‘Before May’ and ‘After May’) are provided in
 separate sheets.
DOI: 10.25402/fsg.16999432
title: Supplementary Table 1b.xlsxSupplementary Tables: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 1b</b>: All frequently
 mutated amino acid residues that have encountered substitutions in 2% or more
 of all SARS-CoV-2 isolates, in at least one country, after May (Group A). The
 frequencies above 2% have been highlighted in ‘red’
DOI: 10.25402/fvl.16999435
title: Supplementary Table 7.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 7</b>: Bi-monthly
 frequencies of the additional Spike protein mutations (frequencies between 2
 to 10%) which overlapped with the experimentally predicted epitopes. The
 mutations which were seen to be increasing as of October are highlighted in
 red.
DOI: 10.25402/fvl.16999438
title: Supplementary Table 3.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 3</b>: Bi-monthly
 frequencies of the highly mutated amino acid residues spanning the months
 from January to October. Each sheet corresponds to a distinct SARS-CoV-2
 protein. The mutational frequencies for each span of two months are provided
 as well as the number of sequences available for this period with which the
 frequencies were computed. The mutations are color-coded as: blue (mutations
 that have occurred with high frequencies in both groups); green (mutations
 that were abundant before May but dwindled in the following months); yellow
 (mutations that were virtually non-existent before May but had gained
 prominence afterwards)
DOI: 10.25402/fvl.16999441
title: Supplementary Table 9.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 9</b>: The additional Spike
 protein mutations which had frequencies ≥ 2% as observed in the period of
 September-October. The mutations previously dealt with in the earlier
 sections have not been listed here.
DOI: 10.25402/fvl.16999444
title: Supplementary Table 8.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 8</b>: The list of computationally predicted S
 protein epitopes, which overlapped with one or more frequently mutated
 residues. The mutations with corresponding countries where they were
 identified are listed. Highly mutated residues are highlighted.
DOI: 10.25402/fvl.16999447
title: Supplementary Table 6.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 6</b>: The list of experimentally determined
 epitopes from which overlapped with one or more frequently mutated residues
 within the Spike protein. The mutations with corresponding countries where
 they were identified are listed. Highly mutated residues are highlighted.
DOI: 10.25402/fvl.16999501
title: Supplementary Table 4.xlsx: Temporal Variations of Country specific mutational profile of SARS-CoV-2: Effect on Vaccine Efficacy

description: <b>Supplementary Table 4</b>: The dominating
 SARS-CoV-2 variants, with at least 10% abundance in respective countries,
 considering the highly mutable amino acid sites. For each strain, the
 positions with substitutions have occurred are filled, while the blank cells
 denote wild-type residues.
DOI: 10.25402/fvl.17206286
title: Supplementary tables 1–7: A systematic review and meta-analysis of the sensitivity of antibody tests for the laboratory confirmation of COVID-19

description: Table S1: Antibody type within 7 days of onset of
 symptoms subgroup meta-analysis heterogeneity
 Table S2: Overall antibody type subgroup
 meta-analysis heterogeneity
 Table S3: Comparison of sensitivity at 7 days*
 Table S4: Comparison of overall
 sensitivity and specificity 
 
 Table S5: Comparison of overall
 sensitivity, specificity as per the test antigen<br>
 Table S6: Summary of specificity and sensitivity 7
 days post symptom onset based on different antigens for CLIA, LFIA and ELISA
 Table S7: Serological test summary of
 overall specificity and sensitivity based on LFIA, CLIA and ELISA
DOI: 10.25402/fvl.19152959
title: Supplementary Tables: Antineutrophil cytoplasmic antibody positivity and clinical implications in COVID-19

description: <b>Supplementary Table 1. </b>ANCA
 status and reasons for ANCA testing in patients.
 <b> </b>
 <b>Supplementary
 Table 2.</b> Comparison of factors that can be
 associated with mortality between ANCA negative and ANCA positive patients
 with mortality.
 
 <b>Supplementary
 Table 3.</b> Distribution of treatment agents used
 for COVID-19 in patients.
DOI: 10.25402/fvl.19519570
title: Reviewing findings on the polypeptide sequence of the SARS-CoV-2 S-protein to discuss the origins of the virus: Supplementary figure.pdf

description: Partial
 alignment among genomes of the coronaviruses RaTG13 and SARS-CoV-2 (accession
 numbers are available in Table 1) and the nucleotide sequence of BtCoV/4991
 (Genbank KP876546.1) [21]. The polypeptide sequence is reported under the
 nucleotide sequences. Alignment of the nucleotide sequences is shown until
 the end of motif C [24] (red). Cyan, polymorphisms between BtCoV/4991 and
 SARS-CoV-2; bold: codon responsible of the amino acid substitution H-to-Y
 occurring between RaTG13 and SARS-CoV-2 (in cyan); green: interacting
 residues of the palm domain according with Gao et al. [24].
DOI: 10.15468/dl.6nzyfm
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Athanas dimorphus Ortmann, 1894"
 ]
}

 The dataset includes 155 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019778-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25402/fvl.19753828
title: Supplementary materials 1: Development of epitope-based chimeric protein as a vaccine against Lujo virus by utilizing immunoinformatic tools

description: Supplementary tables
DOI: 10.25402/fvl.20072972
title: First detection and characterization of EV-A71 and a new genogroup of CVA-24 causing neurological disease in Tunisia: supplementary data

description: Aim: Molecular characterization of enterovirus A71 (EV-A71) and coxsackievirus A24 (CVA-24) strains
isolated during neurological diseases surveillance activities in Tunisian patients. Materials & methods:
Specimens were obtained from two Tunisian children and analyzed for enterovirus with quantitative
reverse transcription PCR (RT-qPCR). We sequenced the whole genome of strains detected. Results: The
EV-A71 sequence reported was assigned to subgenogroup C2 with a high nucleotide sequence identity
to other EV-A71 C2 detected in other countries, which suggests virus migration. Interestingly, in the VP1
coding region, the Tunisian CV-A24 strain displayed high sequence divergence from other CV-A24, which
confirms that it represents a new genogroup. Conclusion: This is the first report of EV-A71 in Tunisia and
the first report of a CV-A24 strain causing aseptic meningitis.
DOI: 10.25402/fvl.20222061
title: Andrographolide induces anti-SARS-CoV-2 response through host-directed mechanism: an in silico study – supplementary data

description: Aim: Considering the present alarming situation of COVID-19 pandemic, we concentrated on evaluating
the efficacy of a novel natural antiviral drug-candidate andrographolide against SARS-CoV-2 through an
in silico model of study. Materials & methods: Interaction of andrographolide against the major host
molecules that are responsible for SARS-CoV-2 pathogenesis were determined using bio-computational
tools, in other words, molecular docking, molecular dynamics simulation and pharmacodynamics–
pharmacokinetics analysis. Result: Computational findings represent that andrographolide efficiently
interacts with the major human–host-associated putative drug-targets of viral-entry points like furin
(-10.54 kcal/mol), TMPRSS-2 (-9.50 kcal/mol), ACE2 (-8.99 kcal/mol) and Cathepsin L (-8.98 kcal/mol).
Moreover, it also blocks the inflammatory regulators including TLR4-MD2 and IL-6, which promote virusinduced
inflammation leading to cytokine storm in the host body. Conclusion: This work elucidates
that, the candidature of andrographolide can be utilized as a potent natural agent for the therapeutic
intervention of SARS-CoV-2 through host-directed treatment.
DOI: 10.25402/fvl.20342667
title: Prevalence of occult hepatitis B infection in liver biopsy sample of patients with nonviral liver disease: Supplementary Figure and Table

description: Aim: To determine the prevalence of occult hepatitis B (HBV) infection (OBI) in patients with nonviral
liver disease. Materials & methods: This study included 83 HBsAg-negative patients followed up at a
gastroenterohepatology clinic. The presence of HBV DNA was investigated by using an in-house nested-
PCR method applied to liver parenchymal biopsy samples obtained from patients who underwent due
nonviral chronic liver disease. Results: OBI was detected in 19 (22.9%) of the 83 cases, in 11 (44%) of 25
anti-HBc-positive patients, and 15 (31.9%) of 47 anti-HBc and/or anti-HBs antibodies-positive patients.
Conclusion: There is a considerable prevalence of OBI among patients with nonviral chronic liver disease.
Therefore, it is suggested that closely monitoring HBV can be useful to prevent or more effectively manage
possible OBI-related complications among patients with nonviral chronic liver disease, especially those
who are HBsAg seronegative or anti-HBV antibody seropositive.
DOI: 10.25402/fvl.20448585
title: Digging for the discovery of SARS-CoV-2 nsp12 inhibitors: a pharmacophore-based and molecular dynamics simulation study: Supplementary tables

description: Aim: COVID-19 is a global health threat. Therapeutics are urgently needed to cure patients severely
infected with COVID-19. Objective: to investigate potential candidates of nsp12 inhibitors by searching
for druggable cavity pockets within the viral protein and drug discovery. Methods: A virtual screening of
ZINC natural products on SARS-CoV-2 nsp12’s druggable cavity was performed. A lead compound with
the highest affinity to nsp12 was simulated dynamically for 10 ns. Results: ZINC03977803 was nominated
as the lead compound. The results showed stable interaction between ZINC03977803 and nsp12 during
10 ns. Discussion: ZINC03977803 showed stable interaction with the catalytic subunit of SARS-CoV-2,
nsp12. It could inhibit the SARS-CoV-2 life cycle by direct interaction with nsp12 and inhibit RdRp complex
formation.
DOI: 10.25402/fvl.22154777
title: Targeting ‘immunogenic hotspots’ in Dengue and Zika virus: an in silico approach to a common vaccine candidate: supplementary figure 1

description: Aim: Dengue and Zika viruses cause significant mortality globally. Considering high sequence similarity
between the viral proteins, we designed common multi-epitope vaccine candidates against these
pathogens. Methods: We identified multiple T and B cell epitope-rich conserved ‘immunogenic hotspots’
from highly antigenic and phylogenetically related viral proteins and used these to design the multiepitope
vaccine (MEV) candidates, ensuring high global population coverage. Results: Four MEV
candidates containing conserved immunogenic hotspots from E and NS5 proteins with the highest
structural integrity could favorably interact with TLR4-MD2 complex in molecular docking studies,
indicating activation of TLR-mediated immune responses. MEVs also induced memory responses in silico,
hallmarks of a good vaccine candidate. Conclusion: Conserved immunogenic hotspots can be utilized to
design cross-protective MEV candidates.
DOI: 10.15468/dl.6fk5rh
title: Occurrence Download

description: A dataset containing 12142287 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Pl@ntNet automatically identified occurrences"
 ]
}

 The dataset includes 12142287 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019760-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25402/fvl.22211317
title: Plasma cytokine profile in occult HBV-infected blood donors: supplementary materials

description: Aim: Cytokine profile in occult HBV infection (OBI) was systematically investigated to identify the
immunopathogenesis of OBI. Materials & methods: A total of 46 OBI, ten asymptomatic hepatitis B surface
antigen carriers, ten chronic hepatitis B and 12 healthy blood donors were recruited. A total of 21 plasma
cytokines were detected. Results: Compared with healthy blood donors, elevated plasma Th1, Th2, Th17
and immune regulatory associated cytokines were observed in OBI. Almost no significant difference was
found for these cytokines among OBI, asymptomatic hepatitis B surface antigen carriers and chronic
hepatitis B. OBI displayed the predominance of type 2 and regulatory immunity. Conclusion: OBI displayed
the general cytokine profile of chronic HBV infection, which might contribute to virus persistence and
the presence of the liver microinflammatory environment. The clinical implications of OBI deserve more
attention.
DOI: 10.25402/fvl.22211317.v1
title: Plasma cytokine profile in occult HBV-infected blood donors: supplementary materials

description: Aim: Cytokine profile in occult HBV infection (OBI) was systematically investigated to identify the
immunopathogenesis of OBI. Materials & methods: A total of 46 OBI, ten asymptomatic hepatitis B surface
antigen carriers, ten chronic hepatitis B and 12 healthy blood donors were recruited. A total of 21 plasma
cytokines were detected. Results: Compared with healthy blood donors, elevated plasma Th1, Th2, Th17
and immune regulatory associated cytokines were observed in OBI. Almost no significant difference was
found for these cytokines among OBI, asymptomatic hepatitis B surface antigen carriers and chronic
hepatitis B. OBI displayed the predominance of type 2 and regulatory immunity. Conclusion: OBI displayed
the general cytokine profile of chronic HBV infection, which might contribute to virus persistence and
the presence of the liver microinflammatory environment. The clinical implications of OBI deserve more
attention.
DOI: 10.25402/fvl.22587730
title: In silico analysis of ACE2 from different animal species provides new insights into SARS-CoV-2 species spillover: supplementary materials

description: Aim: This study aimed to analyze the phylogenetic relationships between the ACE2 of humans and
other animals and investigate the potential interaction between SARS-CoV-2 RBD and ACE2 of different
species. Materials & methods: The phylogenetic construction and molecular interactions were assessed
using computational models. Results & conclusion: Despite the evolutionary distance, 11 species had a
perfect fit for the interaction between their ACE2 and SARS-CoV-2 RBD (Chinchilla lanigera, Neovison
vison, Rhinolophus sinicus, Emballonura alecto, Saccopteryx bilineata, Numida meleagris). Among them,
the avian N. meleagris was reported for the first time in this study as a probable SARS-CoV-2 host due to
the strong molecular interactions. Therefore, predicting potential hosts for SARS-CoV-2 for understanding
the epidemiological cycle and proposal of surveillance strategies
DOI: 10.25402/fvl.23060252
title: In silico assessment of diterpenes as potential inhibitors of SARS-COV-2 main protease: supplementray materials

description: Aim: We aimed to investigate the potential inhibitory effects of diterpenes on SARS-CoV-2 main
protease (Mpro). Materials & methods: We performed a virtual screening of diterpenoids against Mpro
using molecular docking, molecular dynamics simulation and absorption, distribution, metabolism and
excretion) analysis. Results: Some tested compounds followed Lipinski’s rule and showed drug-like
properties. Some diterpenoids possessed remarkable binding affinities with SARS-CoV-2 Mpro and
drug-like pharmacokinetic properties. Three derivatives exhibited structural deviations lower than 1 A˚ .
Conclusion: The findings of the study suggest that some of the diterpenes could be candidates as potential
inhibitors for Mpro of SARS-CoV-2.
DOI: 10.25402/fvl.23301158
title: Cs-GRP78 recognition site on Dengue virus envelope protein: in silico perspective: supplementary table

description: Aim: To understand the binding of the Dengue virus (DENV) envelope and the host cell factor, GRP78.
Materials & methods: In this study, we simulate the binding of the DENV envelope against GRP78
using structural bioinformatics tools. Results: The sequence similarity of the DENV envelope C3–C30
and C302–C333 regions against the Pep42 cyclic peptide suggest these regions are possible recognition
sites for GRP78. C3–C30 has a more similar grand average hydrophobicity index to that of Pep42 and a
more negative binding affinity toward GRP78. Conclusion: We predict this region (C3–C30) of the DENV
envelope to be the recognition site of GRP78. Further experimental validation will be important to future
studies.
DOI: 10.25402/fvl.23301158.v1
title: Cs-GRP78 recognition site on Dengue virus envelope protein: in silico perspective: supplementary table

description: Aim: To understand the binding of the Dengue virus (DENV) envelope and the host cell factor, GRP78.
Materials & methods: In this study, we simulate the binding of the DENV envelope against GRP78
using structural bioinformatics tools. Results: The sequence similarity of the DENV envelope C3–C30
and C302–C333 regions against the Pep42 cyclic peptide suggest these regions are possible recognition
sites for GRP78. C3–C30 has a more similar grand average hydrophobicity index to that of Pep42 and a
more negative binding affinity toward GRP78. Conclusion: We predict this region (C3–C30) of the DENV
envelope to be the recognition site of GRP78. Further experimental validation will be important to future
studies.
DOI: 10.25402/fvl.23804109
title: A single antiviral for a triple epidemic: is itpossible?

description: Aim: A triple epidemic of respiratory syncytial virus (RSV), SARS-CoV-2 and influenza variants is on therise worldwide. It is crucial to identify antiviral agents that can be used against all three viruses associatdwith this triple epidemic. Materials & methods: A total of ten antiviral agents were investigated in thisstudy. Using molecular docking and the molecular mechanics/position-Boltzmann surface area technique,an examination of the binding affinity and protein–ligand interactions was conducted. Results:Out of theten ligands that were compared, three showed the highest affinity for the docking site related to threethe viral infections in descending order: AVG-388, remdesivir and nirmatrelvir. Conclusion: In conclusion,AVG-388, remdesivir and nirmatrelvir could be recommended as effective antiviral agents during the tripleepidemic.