cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25402/fvl.23804109.v1
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.
DOI: 10.25402/fvl.23905068
title: LMP1 encoded by Epstein–Barr virus mayactivate AHR through the ERK pathway innasopharyngeal carcinoma cells: supplementary files

description: Aim: To investigate the role of AHR in nasopharyngeal carcinoma (NPC) and explore the relationshipbetween Epstein–Barr virus (EBV) infection and the AHR pathway. Methods: The effect of LMP1 on theexpression of AHR was analyzed using real-time PCR and western blot. Proliferation and migration of cellswere assessed using CCK8 and Transwell analysis. Results: EBV infection downregulated the expressionof AHR in NPC cells, possibly through activation of the ERK pathway by LMP1 thereby acceleratingAHR proteasomal degradation following translocation to the nucleus. Cell proliferation, migration andautophagy are promoted by activating the AHR pathway. Conclusion: In NPC cells, LMP1 increases thephosphorylation of ERK, which may activate the AHR pathway.
DOI: 10.25402/fvl.23905068.v1
title: LMP1 encoded by Epstein–Barr virus mayactivate AHR through the ERK pathway innasopharyngeal carcinoma cells: supplementary files

description: Aim: To investigate the role of AHR in nasopharyngeal carcinoma (NPC) and explore the relationshipbetween Epstein–Barr virus (EBV) infection and the AHR pathway. Methods: The effect of LMP1 on theexpression of AHR was analyzed using real-time PCR and western blot. Proliferation and migration of cellswere assessed using CCK8 and Transwell analysis. Results: EBV infection downregulated the expressionof AHR in NPC cells, possibly through activation of the ERK pathway by LMP1 thereby acceleratingAHR proteasomal degradation following translocation to the nucleus. Cell proliferation, migration andautophagy are promoted by activating the AHR pathway. Conclusion: In NPC cells, LMP1 increases thephosphorylation of ERK, which may activate the AHR pathway.
DOI: 10.15468/dl.8bs8p8
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "GadmGid is ESP.4_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Eriophorum angustifolium Honck."
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019780-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25402/fsg.24085344
title: Highlighting the role of immune responses,cell death and the nervous system in acuterotavirus infection using weighted geneco-expression network analysis: supplementary tables

description: Aim: Identifying genes and pathways involved in various stages of rotavirus infection could facilitatethe mapping of the interactions between the virus and host. Materials & methods: Weighted geneco-expression network analysis (WGCNA) was employed to construct a co-expression network of genesidentified by microarray analysis from samples from children with acute rotavirus infection. Results: Twospecific modules were most related to rotavirus infection. The analysis of differentially expressed genes(DEGs) disclosed 393 DEGs between normal and infected individuals. Eighteen novel genes were sharedbetween the modules. Conclusion: TheWGCNArevealed novel modules, co-expressed genes and pathwaysinvolved in immune responses, cell death/degradation and the nervous system in acute rotavirus infection.
DOI: 10.25402/fsg.24085344.v1
title: Highlighting the role of immune responses,cell death and the nervous system in acuterotavirus infection using weighted geneco-expression network analysis: supplementary tables

description: Aim: Identifying genes and pathways involved in various stages of rotavirus infection could facilitatethe mapping of the interactions between the virus and host. Materials & methods: Weighted geneco-expression network analysis (WGCNA) was employed to construct a co-expression network of genesidentified by microarray analysis from samples from children with acute rotavirus infection. Results: Twospecific modules were most related to rotavirus infection. The analysis of differentially expressed genes(DEGs) disclosed 393 DEGs between normal and infected individuals. Eighteen novel genes were sharedbetween the modules. Conclusion: TheWGCNArevealed novel modules, co-expressed genes and pathwaysinvolved in immune responses, cell death/degradation and the nervous system in acute rotavirus infection.
DOI: 10.15468/dl.fj3fut
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Athanas dimorphus seedang A.H.Banner & D.M.Banner, 1966"
 ]
}

 The dataset includes 10 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019779-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25402/fvl.24146973
title: Establishment and evaluation of a multiplexPCR amplification-based sequencing methodfor respiratory virus type A: Supplementary data

description: Aim: This study aimed to establish a simple whole-genome sequencing method for respiratory virus typeA (RSVA) used in genomic epidemiological studies. Methods: Multiple primers were designed to amplifyoverlapping amplicons specific to RSVA. The amplicons were sequenced using Illumina and Nanoporesequencing platforms and the sequencing performances of the two platforms were also compared.Results: The study shows that the developed method could recover almost full genomes of RSVA whenCt values were less than 33 for clinical samples. Conclusion: In this study, a whole-genome sequencingmethod was developed for RSVA based on multiplex PCR.
DOI: 10.25402/fvl.24146973.v1
title: Establishment and evaluation of a multiplexPCR amplification-based sequencing methodfor respiratory virus type A: Supplementary data

description: Aim: This study aimed to establish a simple whole-genome sequencing method for respiratory virus typeA (RSVA) used in genomic epidemiological studies. Methods: Multiple primers were designed to amplifyoverlapping amplicons specific to RSVA. The amplicons were sequenced using Illumina and Nanoporesequencing platforms and the sequencing performances of the two platforms were also compared.Results: The study shows that the developed method could recover almost full genomes of RSVA whenCt values were less than 33 for clinical samples. Conclusion: In this study, a whole-genome sequencingmethod was developed for RSVA based on multiplex PCR.
DOI: 10.25402/fvl.24242770
title: Vertical transmission and maternal passiveimmunity post-SARS-CoV-2: supplementary data

description: Since 2020, the highly contagious nature and various transmission routes of SARS-CoV-2 have rendered thepandemic interminable. Vertical transmission (VT) through the placenta and breastmilk, which is frequentfor certain virus types, is thought to exist for SARS-CoV-2 and is hypothesized by many researchers.Conversely, antibodies are produced to counteract the effect of viruses. Since newborns’ immunologicsystem cannot produce proper antibodies, maternal antibodies are usually transferred from mother toinfant/fetus to meet the need. This theory leads to the hypothesis of transmission of antibodies throughthe placenta and breast milk following SARS-CoV-2 infection or vaccination. This paper further discussesthese hypotheses, considering consequences of fetus/infant harm versus benefit.
DOI: 10.25402/fvl.24242770.v1
title: Vertical transmission and maternal passiveimmunity post-SARS-CoV-2: supplementary data

description: Since 2020, the highly contagious nature and various transmission routes of SARS-CoV-2 have rendered thepandemic interminable. Vertical transmission (VT) through the placenta and breastmilk, which is frequentfor certain virus types, is thought to exist for SARS-CoV-2 and is hypothesized by many researchers.Conversely, antibodies are produced to counteract the effect of viruses. Since newborns’ immunologicsystem cannot produce proper antibodies, maternal antibodies are usually transferred from mother toinfant/fetus to meet the need. This theory leads to the hypothesis of transmission of antibodies throughthe placenta and breast milk following SARS-CoV-2 infection or vaccination. This paper further discussesthese hypotheses, considering consequences of fetus/infant harm versus benefit.
DOI: 10.15468/dl.rekrbs
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Luxiaria submonstrata (Walker, 1861)"
 ]
}

 The dataset includes 26 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019781-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25402/fvl.24441718
title: An update on long-acting agents in HIVtherapy: supplementary material

description: Since the advent of highly active antiretroviral therapy, many efforts have been made to broaden thespectrum of possible regimens. Long-acting antiretrovirals, are particularly attractive, since they allow forless frequent dosing and can potentially overcome difficulties associated with daily tablet consumption,including the need for flexibility and privacy. In this article, we present a summary and update on currentlyavailable long-acting antiretrovirals and those under development and discuss issues related to theireffective implementation.
DOI: 10.25402/fvl.24441718.v1
title: An update on long-acting agents in HIVtherapy: supplementary material

description: Since the advent of highly active antiretroviral therapy, many efforts have been made to broaden thespectrum of possible regimens. Long-acting antiretrovirals, are particularly attractive, since they allow forless frequent dosing and can potentially overcome difficulties associated with daily tablet consumption,including the need for flexibility and privacy. In this article, we present a summary and update on currentlyavailable long-acting antiretrovirals and those under development and discuss issues related to theireffective implementation.
DOI: 10.25402/fvl.24466165
title: An update on long-acting agents in HIVtherapy: supplementary data

description: Since the advent of highly active antiretroviral therapy, many efforts have been made to broaden thespectrum of possible regimens. Long-acting antiretrovirals, are particularly attractive, since they allow forless frequent dosing and can potentially overcome difficulties associated with daily tablet consumption,including the need for flexibility and privacy. In this article, we present a summary and update on currentlyavailable long-acting antiretrovirals and those under development and discuss issues related to theireffective implementation.
DOI: 10.25402/fvl.24466165.v1
title: An update on long-acting agents in HIVtherapy: supplementary data

description: Since the advent of highly active antiretroviral therapy, many efforts have been made to broaden thespectrum of possible regimens. Long-acting antiretrovirals, are particularly attractive, since they allow forless frequent dosing and can potentially overcome difficulties associated with daily tablet consumption,including the need for flexibility and privacy. In this article, we present a summary and update on currentlyavailable long-acting antiretrovirals and those under development and discuss issues related to theireffective implementation.
DOI: 10.25402/fvl.24474706
title: Oral bemnifosbuvir (AT-527) vs placebo inpatients with mild-to-moderate COVID-19 inan outpatient setting (MORNINGSKY): supplementary data

description: Aim: This phase III study assessed the efficacy/safety/antiviral activity/pharmacokinetics of bemnifosbuvir,a novel, oral nucleotide analog to treat COVID-19. Patients & methods: Outpatient adults/adolescentswith mild-to-moderate COVID-19 were randomized 2:1 to bemnifosbuvir/placebo. Time to symptomalleviation/improvement (primary outcome), risk of hospitalization/death, viral load and safety wereevaluated. Results: Although the study was discontinued prematurely and did not meet its primary endpoint, bemnifosbuvir treatment resulted in fewer hospitalizations (71% relative risk reduction), COVID-19-related medically attended hospital visits, and COVID-19-related complications compared with placebo.No reduction in viral load was observed. The proportion of patients with adverse events was similar; nodeaths occurred. Conclusion: Bemnifosbuvir showed hospitalization reduction in patients with variabledisease progression risk and was well tolerated.
DOI: 10.25402/fvl.24474706.v1
title: Oral bemnifosbuvir (AT-527) vs placebo inpatients with mild-to-moderate COVID-19 inan outpatient setting (MORNINGSKY): supplementary data

description: Aim: This phase III study assessed the efficacy/safety/antiviral activity/pharmacokinetics of bemnifosbuvir,a novel, oral nucleotide analog to treat COVID-19. Patients & methods: Outpatient adults/adolescentswith mild-to-moderate COVID-19 were randomized 2:1 to bemnifosbuvir/placebo. Time to symptomalleviation/improvement (primary outcome), risk of hospitalization/death, viral load and safety wereevaluated. Results: Although the study was discontinued prematurely and did not meet its primary endpoint, bemnifosbuvir treatment resulted in fewer hospitalizations (71% relative risk reduction), COVID-19-related medically attended hospital visits, and COVID-19-related complications compared with placebo.No reduction in viral load was observed. The proportion of patients with adverse events was similar; nodeaths occurred. Conclusion: Bemnifosbuvir showed hospitalization reduction in patients with variabledisease progression risk and was well tolerated.
DOI: 10.25402/fvl.24711048
title: HIV co-receptor tropism usage: first reportfrom the Iranian patients: supplementary data

description: Aim: The HIV-V3 sequence influences tropism via the interaction of HIV with CCR5 and CXCR4 coreceptors;however, no consistent sequence accounts for R5 or X4-virus. Methods: RT-Nested PCR was performed todefine V3-tropism in 123 samples using genotypic methods, including Geno2Pheno,WebPSSM, PhenoSeq,Net Charge and the 11/25 rule. Results: Among the samples studied, the HIV-1 R5 tropic viruses werepredominant. However, X4 tropism could be a reason for the higher risk of treatment failure. A goodaccordance was observed between paired DNA/RNA tropism results. Conclusion: CCR5 inhibitors can becrucial in simplifying HIV treatment in Iranian patients. X4-virus is a risk factor for treatment failure.Proviral DNA (pvDNA) tropism result can be an appropriate target for V3-tropism determination.
DOI: 10.25402/fvl.24711048.v1
title: HIV co-receptor tropism usage: first reportfrom the Iranian patients: supplementary data

description: Aim: The HIV-V3 sequence influences tropism via the interaction of HIV with CCR5 and CXCR4 coreceptors;however, no consistent sequence accounts for R5 or X4-virus. Methods: RT-Nested PCR was performed todefine V3-tropism in 123 samples using genotypic methods, including Geno2Pheno,WebPSSM, PhenoSeq,Net Charge and the 11/25 rule. Results: Among the samples studied, the HIV-1 R5 tropic viruses werepredominant. However, X4 tropism could be a reason for the higher risk of treatment failure. A goodaccordance was observed between paired DNA/RNA tropism results. Conclusion: CCR5 inhibitors can becrucial in simplifying HIV treatment in Iranian patients. X4-virus is a risk factor for treatment failure.Proviral DNA (pvDNA) tropism result can be an appropriate target for V3-tropism determination.
DOI: 10.25402/fvl.24763491
title: Resistance analysis following sotrovimabtreatment in participants with COVID-19during the phase III COMET-ICE study: supplementary material

description: Aim: Sotrovimab is an engineered human monoclonal antibody that binds a conserved region of theSARS-CoV-2 spike protein. The COMET-ICE phase III study evaluated sotrovimab for treatment of mild tomoderate COVID-19 in nonhospitalized participants with ≥1 risk factor for severe disease progression.Materials & methods: We evaluated the presence of circulating SARS-CoV-2 variants of concern orinterest (VOCs/VOIs) and characterized the presence of baseline, post-baseline and emergent amino acidsubstitutions detected in the epitope of sotrovimab in SARS-CoV-2. Results: None of the sotrovimabtreatedparticipants with baseline epitope substitutions, and 1 of 48 sotrovimab-treated participantswith post-baseline epitope substitutions, met the primary clinical endpoint for progression. Conclusion:Overall, progression was not associated with identified VOC/VOI or the presence of epitope substitutionsin sotrovimab-treated participants.
DOI: 10.25402/fvl.24763491.v1
title: Resistance analysis following sotrovimabtreatment in participants with COVID-19during the phase III COMET-ICE study: supplementary material

description: Aim: Sotrovimab is an engineered human monoclonal antibody that binds a conserved region of theSARS-CoV-2 spike protein. The COMET-ICE phase III study evaluated sotrovimab for treatment of mild tomoderate COVID-19 in nonhospitalized participants with ≥1 risk factor for severe disease progression.Materials & methods: We evaluated the presence of circulating SARS-CoV-2 variants of concern orinterest (VOCs/VOIs) and characterized the presence of baseline, post-baseline and emergent amino acidsubstitutions detected in the epitope of sotrovimab in SARS-CoV-2. Results: None of the sotrovimabtreatedparticipants with baseline epitope substitutions, and 1 of 48 sotrovimab-treated participantswith post-baseline epitope substitutions, met the primary clinical endpoint for progression. Conclusion:Overall, progression was not associated with identified VOC/VOI or the presence of epitope substitutionsin sotrovimab-treated participants.
DOI: 10.25402/fvl.24866418
title: Human RSVA-ON1, the only genotypepresent during 2019–2020 winter season inRiyadh, Saudi Arabia: a retrospective study: supplementary materials

description: Aim: The study aimed to analyze human respiratory syncytial virus (hRSV) strains in nasopharyngealaspirates obtained retrospectively. Materials & methods: Clinical information of ARI patients (n = 53)was accessed and 2nd hypervariable region of G protein gene of RSV was sequenced and analyzed.Results: Cough (98.1%), fever 40 (75.4%) and shortness of breath 32 (60.3%) were the common symptom.Sequence determination (n = 45) categorized all the strains in ON1 genotype. Potential O- and Nglycosylationwere observed at some sites and purifying selections were observed at 274 and 320 codonpositions. Conclusion: The study reports replacement of other RSVA genotypes with ON1. The futurecourse of studies should emphasize on clinical implications of presence of hRSVA-ON1 genotype in a givenpopulation.
DOI: 10.25402/fvl.24866418.v1
title: Human RSVA-ON1, the only genotypepresent during 2019–2020 winter season inRiyadh, Saudi Arabia: a retrospective study: supplementary materials

description: Aim: The study aimed to analyze human respiratory syncytial virus (hRSV) strains in nasopharyngealaspirates obtained retrospectively. Materials & methods: Clinical information of ARI patients (n = 53)was accessed and 2nd hypervariable region of G protein gene of RSV was sequenced and analyzed.Results: Cough (98.1%), fever 40 (75.4%) and shortness of breath 32 (60.3%) were the common symptom.Sequence determination (n = 45) categorized all the strains in ON1 genotype. Potential O- and Nglycosylationwere observed at some sites and purifying selections were observed at 274 and 320 codonpositions. Conclusion: The study reports replacement of other RSVA genotypes with ON1. The futurecourse of studies should emphasize on clinical implications of presence of hRSVA-ON1 genotype in a givenpopulation.
DOI: 10.25402/fvl.24866445
title: Rosmarinic acid inhibits Rift Valley fevervirus: in vitro, computational and analyticalstudies: supplementary materials

description: Aim: The antiviral potentials of rosmarinic acid (RA) against Rift Valley fever (RVF) virus were investigated.Methods: Antiviral activity was investigated by evaluating the reduction in the viral infectivity titer.Computational and LC–MS studies were performed for investigating the mechanism of action. This isvia testing the interaction between RA and its major metabolite with the key infectivity proteins anddetermination of RA cellular permeability. Results: A superior reduction in RVF infectivity titer (45.5%)was observed when RA was applied post-infection compared to 17.7% reduction following its applicationbefore infection in addition to time-dependent inactivation kinetics. Recorded data showed in-silicoinhibitory potential of RA and its metabolite against RVFV cap-binding protein and glycoprotein C, whichare integral for viral transcription. LC–MS revealed cellular inclusion of RA, supporting its intracellularviral interaction. Conclusion: These antiviral potentials might suggest a promising foundation for futureanti-RVF drug development.
DOI: 10.25402/fvl.24866445.v1
title: Rosmarinic acid inhibits Rift Valley fevervirus: in vitro, computational and analyticalstudies: supplementary materials

description: Aim: The antiviral potentials of rosmarinic acid (RA) against Rift Valley fever (RVF) virus were investigated.Methods: Antiviral activity was investigated by evaluating the reduction in the viral infectivity titer.Computational and LC–MS studies were performed for investigating the mechanism of action. This isvia testing the interaction between RA and its major metabolite with the key infectivity proteins anddetermination of RA cellular permeability. Results: A superior reduction in RVF infectivity titer (45.5%)was observed when RA was applied post-infection compared to 17.7% reduction following its applicationbefore infection in addition to time-dependent inactivation kinetics. Recorded data showed in-silicoinhibitory potential of RA and its metabolite against RVFV cap-binding protein and glycoprotein C, whichare integral for viral transcription. LC–MS revealed cellular inclusion of RA, supporting its intracellularviral interaction. Conclusion: These antiviral potentials might suggest a promising foundation for futureanti-RVF drug development.