cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24756924
title: The association between influenza vaccine effectiveness and egg-based manufacturing technology: literature review and US expert consensus

description: Influenza is associated with significant disease burden in the US and is currently best controlled by vaccination programs. Influenza vaccine effectiveness (VE) is low and may be reduced by several factors, including egg adaptations. Although non-egg-based influenza vaccines reportedly have greater VE in egg-adapted seasons, evidence for egg adaptations’ reduction of VE is indirect and dissociated, apart from two previous European consensuses. This study replicated the methodology used in a 2020 literature review and European consensus, providing an updated review and consensus opinion of 10 US experts on the evidence for a mechanistic basis for reduction of VE due to egg-based manufacturing methods. A mechanistic basis was assumed if sufficient evidence was found for underlying principles proposed to give rise to such an effect. Evidence for each principle was brought forward from the 2020 review and identified here by structured literature review and expert panel. Experts rated the strength of support for each principle and a mechanistic basis for reduction of VE due to egg-based influenza vaccine manufacture in a consensus method (consensus for strong/very strong evidence = ≥ 3.5 on 5-point Likert scale). Experts assessed 251 references (from previous study: 185; this study: 66). The majority of references for all underlying principles were rated as strong or very strong supporting evidence (52–86%). Global surveillance, WHO candidate vaccine virus selection, and manufacturing stages involving eggs were identified as most likely to impact influenza VE. After review of extensive evidence for reduction of VE due to egg-based influenza vaccine manufacture, influenza experts in the US joined those in Europe in unanimous agreement for a mechanistic basis for the effect. Vaccine providers and administrators should consider use of non-egg-based influenza vaccine manufacture to reduce the risk of egg adaptations and likely impact on VE.
DOI: 10.6084/m9.figshare.24865121.v2
title: Associations of serum uric acid levels and anthropometric parameters with non-alcoholic fatty liver disease in healthy individuals: innovative insights from a cross-sectional study

description: Non-alcoholic fatty liver disease (NAFLD is a spectrum of liver disease with a rising prevalence, ranging from simple steatosis to steatohepatitis and cirrhosis, where a significant minority face potential complications. Determining the predictive markers plays a crucial role. This study examined the relationship between serum uric acid (SUA) levels and NAFLD in healthy individuals and identified potential other predictors. A cohort of 2162 healthy participants attending routine check-up visits between February 2021 and May 2023 were included. Participants underwent abdominal ultrasound, uric acid measurements, and anthropometric assessments by TANITA. NAFLD was graded using a "hepatic steatosis score." Statistical analysis included nonparametric tests, chi-squared tests, Fisher’s exact test, ROC curve analysis, and logistic regression. The median age was 45 years (range:18-65). 1017 were male, and 1145 were female. Among the participants, 53.9%, 26.3%, 17.9%, and 1.9% exhibited Grade 0, 1, 2, and 3 hepatic steatosis, respectively. ROC analysis showed 80.0% sensitivity and 78.8% specificity for detecting grade 2 or higher hepatic steatosis with a cutoff value of 5.21 mg/dl of SUA (AUC = 0.82, <i>p</i> &lt; 0.001, 95%CI 0.79-0.84). There were significant associations between elevated uric acid levels and NAFLD. Participants with higher body fat percentages, BMI values, and waist-to-hip ratios also demonstrated an increased prevalence of steatosis. Gender significantly influenced liver steatosis, with males exhibiting higher grades compared to females. Logistic regression analysis highlighted positive associations between NAFLD and body fat percentage, waist-to-hip ratio, and uric acid levels. Each unit increase in uric acid levels corresponded to a 2.5-fold increase in the odds of NAFLD (<i>p</i> &lt; 0.001, 95% CI = 2.20-2.84). Our findings suggest a significant relationship between serum uric acid levels and NAFLD in healthy individuals. Elevated uric acid levels, in conjunction with other anthropometric parameters, may serve as potential predictive markers for NAFLD.
DOI: 10.6084/m9.figshare.22352827
title: Characterization of the complete chloroplast genome of <i>Amsonia elliptica</i> (Apocynaceae)

description: <i>Amsonia elliptica</i> (Apocynaceae), endangered species in Korea, is a perennial herb that is economically important as traditional medicine and used as ornamentals. Natural populations of this species are facing extinction due to small population size and isolated distribution. Here, we report the complete chloroplast (cp) genome of <i>A. elliptica</i> using Illumina HiSeq sequencing and its phylogenetic position in subfamily Rauvolfioideae based on 20 Apocynaceae cp genomes. The cp genome of <i>A. elliptica</i> was 154,242 bp in length with a pair of inverted repeats of 25,711 bp, separated by large single-copy and small single-copy regions of 85,382 bp and 17,438 bp, respectively. Our phylogenomic analyses revealed that <i>A. elliptica</i> was closely related to <i>Rhazya stricta</i> in Rauvolfioideae (Apocynaceae).
DOI: 10.6084/m9.figshare.22352827.v1
title: Characterization of the complete chloroplast genome of <i>Amsonia elliptica</i> (Apocynaceae)

description: <i>Amsonia elliptica</i> (Apocynaceae), endangered species in Korea, is a perennial herb that is economically important as traditional medicine and used as ornamentals. Natural populations of this species are facing extinction due to small population size and isolated distribution. Here, we report the complete chloroplast (cp) genome of <i>A. elliptica</i> using Illumina HiSeq sequencing and its phylogenetic position in subfamily Rauvolfioideae based on 20 Apocynaceae cp genomes. The cp genome of <i>A. elliptica</i> was 154,242 bp in length with a pair of inverted repeats of 25,711 bp, separated by large single-copy and small single-copy regions of 85,382 bp and 17,438 bp, respectively. Our phylogenomic analyses revealed that <i>A. elliptica</i> was closely related to <i>Rhazya stricta</i> in Rauvolfioideae (Apocynaceae).
DOI: 10.6084/m9.figshare.22256246
title: The complete mitochondrial genome of a wild-collected <i>Kappaphycus malesianus</i> (Solieriaceae, Rhodophyta)

description: <i>Kappaphycus malesianus</i> is a red seaweed farmed primarily for its carrageenan, a polysaccharide important in the food and pharmaceutical industries. Among the commercially cultivated <i>Kappaphycus</i> species, only <i>K. malesianus</i> has no mitogenome data available. Here, we assembled the mitochondrial genome of <i>K. malesianus</i> from next-generation sequencing data. The circular mitogenome consisted of 25,250 base pairs (bp) with a GC content of 30.25%. These values were comparable to previously sequenced solieriacean mitogenomes. Structural features, such as the stem-loop and hairpin, which were previously reported in other rhodophytes mitochondrial DNA, were also identified. The annotated genes (24 protein-coding genes, 24 tRNA genes, and 2 rRNA genes) were arranged in an order similar to the other available solieriacean mitogenomes. Lastly, phylogenetic analysis using 23 predicted protein domains showed the sister relationship of <i>K. malesianus</i> with other <i>Kappaphycus</i> species.
DOI: 10.6084/m9.figshare.22352822
title: The complete chloroplast genome of <i>Ligusticopsis acaulis</i> (Shan et Sheh) Pimenov (Apiaceae), an endemic species from China

description: <i>Ligusticopsis acaulis</i>, belonging to the family Apiaceae (Umbelliferae), is endemic to China. The complete chloroplast genome sequence of <i>L. acaulis</i> was assembled and annotated for the first time in this study. The results showed that the plastome was 148,509 bp in length and consisted of a pair of inverted repeat regions (IRs: 19,468 bp), a large single-copy region (LSC: 91,902 bp), and a small single-copy region (SSC: 17,671 bp). A total of 114 unique genes were annotated, including 80 protein-coding, 30 tRNA, and four rRNA genes. According to the phylogenetic analysis, <i>L. acaulis</i> belongs to the tribe Selineae, with a close relationship to <i>Ligusticum hispidum</i> (Franch.) Wolff.
DOI: 10.6084/m9.figshare.22352822.v1
title: The complete chloroplast genome of <i>Ligusticopsis acaulis</i> (Shan et Sheh) Pimenov (Apiaceae), an endemic species from China

description: <i>Ligusticopsis acaulis</i>, belonging to the family Apiaceae (Umbelliferae), is endemic to China. The complete chloroplast genome sequence of <i>L. acaulis</i> was assembled and annotated for the first time in this study. The results showed that the plastome was 148,509 bp in length and consisted of a pair of inverted repeat regions (IRs: 19,468 bp), a large single-copy region (LSC: 91,902 bp), and a small single-copy region (SSC: 17,671 bp). A total of 114 unique genes were annotated, including 80 protein-coding, 30 tRNA, and four rRNA genes. According to the phylogenetic analysis, <i>L. acaulis</i> belongs to the tribe Selineae, with a close relationship to <i>Ligusticum hispidum</i> (Franch.) Wolff.
DOI: 10.6084/m9.figshare.22256246.v1
title: The complete mitochondrial genome of a wild-collected <i>Kappaphycus malesianus</i> (Solieriaceae, Rhodophyta)

description: <i>Kappaphycus malesianus</i> is a red seaweed farmed primarily for its carrageenan, a polysaccharide important in the food and pharmaceutical industries. Among the commercially cultivated <i>Kappaphycus</i> species, only <i>K. malesianus</i> has no mitogenome data available. Here, we assembled the mitochondrial genome of <i>K. malesianus</i> from next-generation sequencing data. The circular mitogenome consisted of 25,250 base pairs (bp) with a GC content of 30.25%. These values were comparable to previously sequenced solieriacean mitogenomes. Structural features, such as the stem-loop and hairpin, which were previously reported in other rhodophytes mitochondrial DNA, were also identified. The annotated genes (24 protein-coding genes, 24 tRNA genes, and 2 rRNA genes) were arranged in an order similar to the other available solieriacean mitogenomes. Lastly, phylogenetic analysis using 23 predicted protein domains showed the sister relationship of <i>K. malesianus</i> with other <i>Kappaphycus</i> species.
DOI: 10.6084/m9.figshare.22232032
title: Complete chloroplast and mitochondrial genomes of <i>Ditrichum rhynchostegium</i> Kindb. (Ditrichaceae, Bryophyta)

description: The moss family Pottiaceae is one of the most diverse lineages of the subclass Dicranidae (haplolepideous mosses). Nevertheless, the phylogenetic relationships of Pottiaceae with other Dicranidae families remain unclear. To better understand the ancestral genomic structure and evolution of the Pottiaceae, herein, we present the chloroplast and mitochondrial genomes of <i>Ditrichum rhynchostegium</i> (Ditrichaceae, Bryophyta). The chloroplast genome is 124,628 bp long and displayed a circular structure composed of a large single-copy region, a small single-copy region, and a pair of inverted repeats. It has 118 genes, including 82 protein-coding genes, 32 tRNA genes, and four rRNA genes. The mitochondrial genome is 106,246 bp long and has a circular structure. It contains 67 genes, including 40 protein-coding genes, 24 tRNA genes, and three rRNA genes. Phylogenetic trees based on the coding sequences strongly support the sister relationship of <i>D. rhynchostegium</i> with all Pottiaceous accessions, and the dextrosely arranged operculum cells suggest its affinity for Pottiaceae. This study also demonstrates that long-read sequencing employing the Nanopore platform facilitates the repair of unassembled or misassembled organellar genomic regions.
DOI: 10.6084/m9.figshare.22193202
title: Complete chloroplast genome sequence of <i>Solanum iopetalum</i>, one of the tuber-bearing wild potato relatives

description: <i>Solanum iopetalum</i> belongs to the Solanaceae family and is one of the tuber-bearing wild <i>Solanum</i> species. In this study, chloroplast genome sequencing of the species, completed with Illumina sequencing technology, is presented. The length of the chloroplast genome is 155,625 bp with a GC content of 37.86%. It comprises a large single copy (LSC) region of 86,057 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,593 bp. Additionally, 158 functional genes in the genome are identified, including 105 protein-coding genes, 8 ribosomal RNAs, and 45 transfer RNAs. Phylogenetic analysis revealed that <i>S. iopetalum</i> is grouped into a large clade with other <i>Solanum</i> species, including cultivated potatoes (<i>S. tuberosum</i>) and is closely related to Mexican <i>Solanum</i> species (<i>S. stoloniferum</i>, <i>S. verrucosum</i>, <i>S. hougasii</i>, <i>S. hjertingii</i>, and <i>S. demissum</i>). This study provides useful genomic information for future breeding and evolutionary studies of <i>S. iopetalum</i> and other <i>Solanum</i> species.
DOI: 10.6084/m9.figshare.22193202.v1
title: Complete chloroplast genome sequence of <i>Solanum iopetalum</i>, one of the tuber-bearing wild potato relatives

description: <i>Solanum iopetalum</i> belongs to the Solanaceae family and is one of the tuber-bearing wild <i>Solanum</i> species. In this study, chloroplast genome sequencing of the species, completed with Illumina sequencing technology, is presented. The length of the chloroplast genome is 155,625 bp with a GC content of 37.86%. It comprises a large single copy (LSC) region of 86,057 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,593 bp. Additionally, 158 functional genes in the genome are identified, including 105 protein-coding genes, 8 ribosomal RNAs, and 45 transfer RNAs. Phylogenetic analysis revealed that <i>S. iopetalum</i> is grouped into a large clade with other <i>Solanum</i> species, including cultivated potatoes (<i>S. tuberosum</i>) and is closely related to Mexican <i>Solanum</i> species (<i>S. stoloniferum</i>, <i>S. verrucosum</i>, <i>S. hougasii</i>, <i>S. hjertingii</i>, and <i>S. demissum</i>). This study provides useful genomic information for future breeding and evolutionary studies of <i>S. iopetalum</i> and other <i>Solanum</i> species.
DOI: 10.6084/m9.figshare.22232032.v1
title: Complete chloroplast and mitochondrial genomes of <i>Ditrichum rhynchostegium</i> Kindb. (Ditrichaceae, Bryophyta)

description: The moss family Pottiaceae is one of the most diverse lineages of the subclass Dicranidae (haplolepideous mosses). Nevertheless, the phylogenetic relationships of Pottiaceae with other Dicranidae families remain unclear. To better understand the ancestral genomic structure and evolution of the Pottiaceae, herein, we present the chloroplast and mitochondrial genomes of <i>Ditrichum rhynchostegium</i> (Ditrichaceae, Bryophyta). The chloroplast genome is 124,628 bp long and displayed a circular structure composed of a large single-copy region, a small single-copy region, and a pair of inverted repeats. It has 118 genes, including 82 protein-coding genes, 32 tRNA genes, and four rRNA genes. The mitochondrial genome is 106,246 bp long and has a circular structure. It contains 67 genes, including 40 protein-coding genes, 24 tRNA genes, and three rRNA genes. Phylogenetic trees based on the coding sequences strongly support the sister relationship of <i>D. rhynchostegium</i> with all Pottiaceous accessions, and the dextrosely arranged operculum cells suggest its affinity for Pottiaceae. This study also demonstrates that long-read sequencing employing the Nanopore platform facilitates the repair of unassembled or misassembled organellar genomic regions.
DOI: 10.6084/m9.figshare.22292673
title: The complete mitochondrial genome of <i>Anthrenus museorum</i> (Coleoptera: Bostrichiformia: Dermestidae) from China

description: Dermestid beetles (Coleoptera: Bostrichiformia: Dermestidae) are important pests of various storage products and pose a potential threat to international trade. In this study, the whole mitogenome of <i>Anthrenus museorum</i> was first sequenced and annotated and was found to have the same gene order observed in known dermestid beetles. It comprised 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs and a control region. The typical ATN start codon was observed in all PCGs, except for <i>ND3</i> (TTG), and all 13 PCGs showed three types of stop codons (TAA, TAG, and T-). Phylogenetic analysis based on the PCGs indicated that the relationships within Bostrichiformia were reconstructed, with the exception of one early emerging species of Bostrichidae that actually makes the group polyphyletic, as (Dermestidae + (Bostrichidae + Anobiidae)). Moreover, it revealed a close relationship between <i>A. museorum</i> and <i>A. verbasci</i> using maximum likelihood and Bayesian inference analysis.
DOI: 10.6084/m9.figshare.22292673.v1
title: The complete mitochondrial genome of <i>Anthrenus museorum</i> (Coleoptera: Bostrichiformia: Dermestidae) from China

description: Dermestid beetles (Coleoptera: Bostrichiformia: Dermestidae) are important pests of various storage products and pose a potential threat to international trade. In this study, the whole mitogenome of <i>Anthrenus museorum</i> was first sequenced and annotated and was found to have the same gene order observed in known dermestid beetles. It comprised 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs and a control region. The typical ATN start codon was observed in all PCGs, except for <i>ND3</i> (TTG), and all 13 PCGs showed three types of stop codons (TAA, TAG, and T-). Phylogenetic analysis based on the PCGs indicated that the relationships within Bostrichiformia were reconstructed, with the exception of one early emerging species of Bostrichidae that actually makes the group polyphyletic, as (Dermestidae + (Bostrichidae + Anobiidae)). Moreover, it revealed a close relationship between <i>A. museorum</i> and <i>A. verbasci</i> using maximum likelihood and Bayesian inference analysis.
DOI: 10.6084/m9.figshare.22336409
title: Complete mitochondrial genome of <i>Belligobio pengxianensis</i> (Cypriniformes: Gobionidae)

description: <i>Belligobio pengxianensis</i> is a small fish endemic to the upper Yangtze River of China. In this study, the complete mitochondrial genome of <i>B. pengxianensis</i> is determined for the first time, and it should become a reference sequence to aid in species identification, biodiversity monitoring and conservation. The mitogenome has overall length of 16,610 bp and AT content of 55.23%, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one non-coding control region. The results of phylogenetic analyses show that <i>B. pengxianensis</i> is nested within the genus <i>Hemibarbus</i>.
DOI: 10.6084/m9.figshare.22336409.v1
title: Complete mitochondrial genome of <i>Belligobio pengxianensis</i> (Cypriniformes: Gobionidae)

description: <i>Belligobio pengxianensis</i> is a small fish endemic to the upper Yangtze River of China. In this study, the complete mitochondrial genome of <i>B. pengxianensis</i> is determined for the first time, and it should become a reference sequence to aid in species identification, biodiversity monitoring and conservation. The mitogenome has overall length of 16,610 bp and AT content of 55.23%, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one non-coding control region. The results of phylogenetic analyses show that <i>B. pengxianensis</i> is nested within the genus <i>Hemibarbus</i>.
DOI: 10.6084/m9.figshare.22352819
title: The complete mitochondrial genome of <i>Peleteria iavana</i> (Diptera, Tachinidae) in Guizhou, China, and its phylogenetic placement

description: The mitochondrial genome of the tachinid fly <i>Peleteria iavana</i> (Wiedemann, 1819), which belongs to the family Tachinidae, was obtained for the first time using high-throughput sequencing techniques. The complete mitochondrial genome is 15,697 bp in size and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNAs and a non-coding control region. The nucleotide composition biases A and T, the overall A + T percentage is up to 78.9% of the entire mitogenome. A phylogenetic analysis of 30 species within the family Tachinidae suggested that <i>P. iavana</i> is most closely related to (<i>Janthinomyia</i> sp.+<i>Lydina aenea</i>). The <i>P. iavana</i> mitochondrial genome will be a fundamental resource for understanding the molecular phylogenetic relationships of the species-rich subfamily Tachininae of Tachinidae.
DOI: 10.6084/m9.figshare.22352819.v1
title: The complete mitochondrial genome of <i>Peleteria iavana</i> (Diptera, Tachinidae) in Guizhou, China, and its phylogenetic placement

description: The mitochondrial genome of the tachinid fly <i>Peleteria iavana</i> (Wiedemann, 1819), which belongs to the family Tachinidae, was obtained for the first time using high-throughput sequencing techniques. The complete mitochondrial genome is 15,697 bp in size and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNAs and a non-coding control region. The nucleotide composition biases A and T, the overall A + T percentage is up to 78.9% of the entire mitogenome. A phylogenetic analysis of 30 species within the family Tachinidae suggested that <i>P. iavana</i> is most closely related to (<i>Janthinomyia</i> sp.+<i>Lydina aenea</i>). The <i>P. iavana</i> mitochondrial genome will be a fundamental resource for understanding the molecular phylogenetic relationships of the species-rich subfamily Tachininae of Tachinidae.
DOI: 10.6084/m9.figshare.22302781
title: Complete mitochondrial genome sequence and annotation of <i>Rhinogobius lentiginis</i> (Gobiiformes: Gobiidae: Gobionellinae)

description: We report the complete mitochondrial genome of <i>Rhinogobius lentiginis</i>, which was found to be a circular molecule of 16,633 bp in length and included 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding control region. The overall base composition was 28.44% A, 26.21% T, 16.33% G, and 29.02% C. Phylogenetic analyses using maximum-likelihood and Bayesian inference methods revealed a close genome relationship among <i>R. lentiginis</i>, <i>R. niger</i>, <i>R. shennongensis</i> and <i>R. maculagenys</i>. The complete mitogenome of <i>R. lentiginis</i> will provide a valuable resource for species classification and conservation.
DOI: 10.6084/m9.figshare.22302781.v1
title: Complete mitochondrial genome sequence and annotation of <i>Rhinogobius lentiginis</i> (Gobiiformes: Gobiidae: Gobionellinae)

description: We report the complete mitochondrial genome of <i>Rhinogobius lentiginis</i>, which was found to be a circular molecule of 16,633 bp in length and included 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding control region. The overall base composition was 28.44% A, 26.21% T, 16.33% G, and 29.02% C. Phylogenetic analyses using maximum-likelihood and Bayesian inference methods revealed a close genome relationship among <i>R. lentiginis</i>, <i>R. niger</i>, <i>R. shennongensis</i> and <i>R. maculagenys</i>. The complete mitogenome of <i>R. lentiginis</i> will provide a valuable resource for species classification and conservation.