90 results on '"Kuo LY"'
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2. A DNA barcode reference of Asian ferns with expert-identified voucher specimens and DNA samples.
- Author
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Kuo LY, Tang SK, Huang YH, Xie PJ, Chen CW, Chang ZX, Hsu TC, Chang YH, Chao YS, Chen CW, Fawcett S, Nitta JH, Sundue M, Kao TT, Luu HT, Mustapeng AMA, Coritico FP, Amoroso VB, and Thai YK
- Subjects
- DNA, Plant genetics, DNA Barcoding, Taxonomic, Ferns genetics, Ferns classification, Biodiversity, Phylogeny
- Abstract
Ferns belong to species-rich group of land plants, encompassing more than 11,000 extant species, and are crucial for reflecting terrestrial ecosystem changes. However, our understanding of their biodiversity hotspots, particularly in Southeast Asia, remains limited due to scarce genetic data. Despite harboring around one-third of the world's fern species, less than 6% of Southeast Asian ferns have been DNA-sequenced. In this study, we addressed this gap by sequencing 1,496 voucher-referenced and expert-identified fern samples from (sub)tropical Asia, spanning Malaysia, the Philippines, Taiwan, and Vietnam, to retrieve their rbcL and trnL-F sequences. This DNA barcode collection of Asian ferns encompasses 956 species across 152 genera and 34 families, filling major gaps in fern biodiversity understanding and advancing research in systematics, phylogenetics, ecology and conservation. This dataset significantly expands the Fern Tree of Life to over 6,000 species, serving as a pivotal and global reference for worldwide barcoding identification of ferns., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
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3. Comparison of perioperative bleeding risk between direct oral anticoagulants in transurethral resection of prostate.
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Kuo LY, Kuo J, Silverman J, Kim JJY, Letch C, and McClintock S
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- Humans, Male, Retrospective Studies, Aged, Middle Aged, Postoperative Hemorrhage chemically induced, Postoperative Hemorrhage epidemiology, Warfarin adverse effects, Warfarin administration & dosage, Administration, Oral, Pyridones adverse effects, Pyridones administration & dosage, Thromboembolism prevention & control, Thromboembolism epidemiology, Thromboembolism etiology, Rivaroxaban adverse effects, Rivaroxaban administration & dosage, Pyrazoles adverse effects, Pyrazoles administration & dosage, Aged, 80 and over, Transurethral Resection of Prostate adverse effects, Prostatic Hyperplasia surgery, Prostatic Hyperplasia drug therapy, Prostatic Hyperplasia complications, Anticoagulants adverse effects, Anticoagulants administration & dosage
- Abstract
Objectives: To evaluate the perioperative morbidity and mortality associated with direct oral anticoagulants (DOACs) and warfarin for patients receiving transurethral resection of prostate (TURP)., Patients and Methods: This was a single-centre, retrospective cohort analysis of patients who underwent TURP for benign prostate hyperplasia from April 2019 to December 2023. The primary objective was to evaluate the perioperative bleeding and thromboembolic risk between anticoagulated (AC) vs no-AC patients. The secondary objective was to evaluate perioperative bleeding and thromboembolic risk between different formulations of DOACs. Patient demographics, prior treatment, prostate size, baseline bleeding risk, and operative details were collected. Bleeding and thromboembolic-related morbidity were captured within a 3-month postoperative period. Perioperative management of AC therapy was recorded, and all patients had their AC therapy withheld. Cohort characteristic between the AC vs no-AC, and DOAC groups were analysed with two-sided t-test, and chi-square test. Further logistic regression analyses were carried out to identified significant variables between the groups. These significant variables were used for adjustment in inverse probability-weighted treatment effect analysis to evaluate bleeding risk., Results: There were 629 patients in the cohort, and 113 (18%) patients were receiving AC therapy. The AC patients were at 1.6 times statistically significant increased risk of acute bleeding, and 11 times increased risk of prolonged haematuria for >14 days. When compared to apixaban, patients on rivaroxaban conferred a statistically significant increased risk of acute bleeding by 2.21 times. Patients receiving AC therapy had a statistically significant increased risk of stroke in the perioperative setting (no-AC vs AC: 0.4% vs 2.7%, P = 0.01)., Conclusion: This is the first study to evaluate risk of bleeding for TURP patients receiving DOACs. The AC patients are more likely to experience haematuria and stroke in the perioperative period despite withholding therapy. Apixaban appears to cause less bleeding-related complications than rivaroxaban., (© 2024 The Author(s). BJU International published by John Wiley & Sons Ltd on behalf of BJU International.)
- Published
- 2024
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4. Historical Article: Settling the Dispute of Romantic Composer Bedřich Smetana's Neurological Deterioration.
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Hsiao YS, Kuo LY, Chin CY, and Hsiao SC
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- 2024
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5. An efficient and effective RNA extraction protocol for ferns.
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Pelosi JA, Davenport R, Barbazuk WB, Sessa EB, and Kuo LY
- Abstract
Premise: The extraction of high-quality RNA is the critical first step for the analysis of gene expression and gene space. This remains particularly challenging in plants, and especially in ferns, where the disruption of the cell wall and separation of organic compounds from nucleic acids is not trivial., Methods: We developed a cetyltrimethylammonium bromide (CTAB)-based RNA extraction protocol that consistently performs well across a large phylogenetic breadth of ferns-a lineage of plants high in secondary compounds-and in an array of tissue types. Two alternative options (precipitation vs. clean-up without intermediate precipitation) are presented, both of which yield high-quality RNA extracts with optical density (OD) ratios of OD 260/280 = 1.9-2.1 and OD 260/230 > 1.6, and RNA integrity numbers >7., Conclusions: This study presents an efficient protocol for the extraction of high-quality RNA from multiple tissues and across the fern phylogeny, a clade of plants that still lags behind other major lineages in the development of genomic resources. We hope that this method can be used to help facilitate the closing of this gap., (© 2024 The Author(s). Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2024
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6. The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae.
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Tseng YH, Kuo LY, Borokini I, and Fawcett S
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- Polyploidy, Hybridization, Genetic, Ferns genetics, Ferns classification, Genetic Speciation, Phylogeny
- Abstract
Premise: Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape., Methods: By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework., Results: We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other., Conclusions: The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages., (© 2024 The Author(s). American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2024
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7. Doping-Induced Surface and Grain Boundary Effects in Ni-Rich Layered Cathode Materials.
- Author
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Kuo LY, Roitzheim C, Valencia H, Mayer J, Möller S, Myung ST, Finsterbusch M, Guillon O, Fattakhova-Rohlfing D, and Kaghazchi P
- Abstract
In this work, the effects of dopant size and oxidation state on the structure and electrochemical performance of LiNi
0.8 Co0.1 Mn0.1 O2 (NCM811) are investigated. It is shown that doping with boron (B) which has a small ionic radius and an oxidation state of 3+, leads to the formation of a boron oxide-containing surface coating (probably Li3 BO3 ), mainly on the outer surface of the secondary particles. Due to this effect, boron only slightly affects the size of the primary particle and the initial capacity, but significantly improves the capacity retention. On the other hand, the dopant ruthenium (Ru) with a larger ionic radius and a higher oxidation state of 5+ can be stabilized within the secondary particles and does not experience a segregation to the outer agglomerate surface. However, the Ru dopant preferentially occupies incoherent grain boundary sites, resulting in smaller primary particle size and initial capacity than for the B-doped and pristine NCM811. This work demonstrates that a small percentage of dopant (2 mol%) cannot significantly affect bulk properties, but it can strongly influence the surface and/or grain boundary properties of microstructure and thus the overall performance of cathode materials., (© 2024 The Authors. Small published by Wiley‐VCH GmbH.)- Published
- 2024
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8. Ablation of specific insulin-like growth factor I forms reveals the importance of cleavage for regenerative capacity and glycosylation for skeletal muscle storage.
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Luo YE, Villani KR, Lei H, Kuo LY, Imery I, Stoker BE, Fatima N, Noles SM, Moore CM, and Barton ER
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- Animals, Glycosylation, Mice, Mice, Inbred C57BL, Male, Female, Insulin-Like Growth Factor I metabolism, Insulin-Like Growth Factor I genetics, Muscle, Skeletal metabolism, Regeneration physiology
- Abstract
Insulin-like growth factor-I (IGF-I) facilitates mitotic and anabolic actions in all tissues. In skeletal muscle, IGF-I can promote growth and resolution of damage by promoting satellite cell proliferation and differentiation, suppressing inflammation, and enhancing fiber formation. While the most well-characterized form of IGF-I is the mature protein, alternative splicing and post-translational modification complexity lead to several additional forms of IGF-I. Previous studies showed muscle efficiently stores glycosylated pro-IGF-I. However, non-glycosylated forms display more efficient IGF-I receptor activation in vitro, suggesting that the removal of the glycosylated C terminus is a necessary step to enable increased activity. We employed CRISPR-Cas9 gene editing to ablate IGF-I glycosylation sites (2ND) or its cleavage site (3RA) in mice to determine the necessity of glycosylation or cleavage for IGF-I function in postnatal growth and during muscle regeneration. 3RA mice had the highest circulating and muscle IGF-I content, whereas 2ND mice had the lowest levels compared to wild-type mice. After weaning, 4-week-old 2ND mice exhibited higher body and skeletal muscle mass than other strains. However, by 16 weeks of age, muscle and body size differences disappeared. Even though 3RA mice had more IGF-I stored in muscle in homeostatic conditions, regeneration was delayed after cardiotoxin-induced injury, with prolonged necrosis most evident at 5 days post injury (dpi). In contrast, 2ND displayed improved regeneration with reduced necrosis, and greater fiber size and muscle mass at 11 and 21 dpi. Overall, these results demonstrate that while IGF-I glycosylation may be important for storage, cleavage is needed to enable IGF-I to be used for efficient activity in postnatal growth and following acute injury., (© 2024 The Authors. The FASEB Journal published by Wiley Periodicals LLC on behalf of Federation of American Societies for Experimental Biology.)
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- 2024
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9. Systematics and evolutionary dynamics of insect-fern interactions in the specialized fern-spore feeding Cuprininae (Lepidoptera, Stathmopodidae).
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Shen ZY, Terada T, Landry JF, Hoare RJB, Kuo LY, Chou MH, Hsu YF, and Huang JP
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- Animals, Phylogeny, Insecta, Spores, Lepidoptera genetics, Ferns
- Abstract
Fern-spore-feeding (FSF) is rare and found in only four families of Lepidoptera. Stathmopodidae is the most speciose family that contains FSF species, and its subfamily Cuprininae exclusively specializes on FSF. However, three species of Stathmopodinae also specialize on FSF. To better understand the evolutionary history of FSF and, more generally, the significance of specialization on a peculiar host, a phylogenetic and taxonomic revision for this group is necessary. We reconstructed the most comprehensive molecular phylogeny, including one mitochondrial and four nuclear genes, of Stathmopodidae to date, including 137 samples representing 62 species, with a particular focus on the FSF subfamily, Cuprininae, including 33 species (41% of named species) from 6 of the 7 Cuprininae genera. Species from two other subfamilies, Stathmopodinae and Atkinsoniinae, were also included. We found that FSF evolved only once in Stathmopodidae and that the previous hypothesis of multiple origins of FSF was misled by inadequate taxonomy. Moreover, we showed that (1) speciation/extinction rates do not differ significantly between FSF and non-FSF groups and that (2) oligophage is the ancestral character state in Cuprininae. We further revealed that a faster rate of accumulating specialists over time, and thus a higher number of specialists, was achieved by a higher transition rate from oligophagages to specialists compared to the transition rate in the opposite direction. We finish by describing three new genera, Trigonodagen. nov., Petalagen. nov., and Pediformisgen. nov., and revalidating five genera: Cuprina, Calicotis, Thylacosceles, Actinoscelis, Thylacosceloides in Cuprininae, and we provide an updated taxonomic key to genera and a revised global checklist of Cuprininae., (Copyright © 2024 Elsevier Inc. All rights reserved.)
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- 2024
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10. Two birds with one stone: One-pot concurrent Ta-doping and -coating on Ni-rich LiNi 0.92 Co 0.04 Mn 0.04 O 2 cathode materials with fiber-type microstructure and Li + -conducting layer formation.
- Author
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Hendri YB, Kuo LY, Seenivasan M, Wu YS, Wu SH, Chang JK, Jose R, Ihrig M, Kaghazchi P, and Yang CC
- Abstract
A novel scalable Taylor-Couette reactor (TCR) synthesis method was employed to prepare Ta-modified LiNi
0.92 Co0.04 Mn0.04 O2 (T-NCM92) with different Ta contents. Through experiments and density functional theory (DFT) calculations, the phase and microstructure of Ta-modified NCM92 were analyzed, showing that Ta provides a bifunctional (doping and coating at one time) effect on LiNi0.92 Co0.04 Mn0.04 O2 cathode material through a one-step synthesis process via a controlling suitable amount of Ta and Li-salt. Ta doping allows the tailoring of the microstructure, orientation, and morphology of the primary NCM92 particles, resulting in a needle-like shape with fine structures that considerably enhance Li+ ion diffusion and electrochemical charge/discharge stability. The Ta-based surface-coating layer effectively prevented microcrack formation and inhibited electrolyte decomposition and surface-side reactions during cycling, thereby significantly improving the electrochemical performance and long-term cycling stability of NCM92 cathodes. Our as-prepared NCM92 modified with 0.2 mol% Ta (i.e., T2-NCM92) exhibits outstanding cyclability, retaining 84.5 % capacity at 4.3 V, 78.3 % at 4.5 V, and 67.6 % at 45 ℃ after 200 cycles at 1C. Even under high-rate conditions (10C), T2-NCM92 demonstrated a remarkable capacity retention of 66.9 % after 100 cycles, with an initial discharge capacity of 157.6 mAh g-1 . Thus, the Ta modification of Ni-rich NCM92 materials is a promising option for optimizing NCM cathode materials and enabling their use in real-world electric vehicle (EV) applications., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)- Published
- 2024
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11. Prevalent arbuscular mycorrhizae in roots and highly variable mycobiome in leaves of epiphytic subtropical fern Ophioderma pendulum.
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Xie QY, Kuo LY, Chang CC, Lin CJ, Wang WH, and Chen KH
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Premise: Endophytic and mycorrhizal fungi are crucial in facilitating plant nutrition acquisition and stress tolerance. In epiphytic habitats, plants face nutrition and water stress, but their roots are mostly nonmycorrhizal and especially lacking in arbuscular mycorrhizal associations. Ophioderma pendulum is an epiphytic fern with a partially mycoheterotrophic lifestyle, likely heavily reliant on symbiotic fungi. To characterize fungal associations in the sporophyte of O. pendulum, we focused on leaves and roots of O. pendulum, seeking to reveal the fungal communities in these organs., Methods: Roots and leaves from O. pendulum in a subtropical forest were examined microscopically to observe the morphology of fungal structures and determine the percentage of various fungal structures in host tissues. Fungal composition was profiled using metabarcoding techniques that targeted ITS2 of the nuclear ribosomal DNA., Results: Roots were consistently colonized by arbuscular mycorrhizal fungi (Glomeromycota), especially Acaulospora. Unlike previous findings on epiphytic ferns, dark septate endophytes were rare in O. pendulum roots. Leaves were predominantly colonized by Ascomycota fungi, specifically the classes Dothideomycetes (46.88%), Eurotiomycetes (11.51%), Sordariomycetes (6.23%), and Leotiomycetes (6.14%). Across sampling sites, fungal community compositions were similar in the roots but differed significantly in the leaves., Conclusions: Ophioderma pendulum maintains stable, single-taxon-dominant communities in the roots, primarily featuring arbuscular mycorrhizal fungi, whereas the leaves may harbor opportunistic fungal colonizers. Our study underlines the significance of mycorrhizal fungi in the adaptation of epiphytic ferns., (© 2024 Botanical Society of America.)
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- 2024
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12. Author Correction: The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence.
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Huang X, Wang W, Gong T, Wickell D, Kuo LY, Zhang X, Wen J, Kim H, Lu F, Zhao H, Chen S, Li H, Wu W, Yu C, Chen S, Fan W, Chen S, Bao X, Li L, Zhang D, Jiang L, Khadka D, Yan X, Liao Z, Zhou G, Guo Y, Ralph J, Sederoff RR, Wei H, Zhu P, Li FW, Ming R, and Li Q
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- 2024
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13. Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes.
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Li C, Wickell D, Kuo LY, Chen X, Nie B, Liao X, Peng D, Ji J, Jenkins J, Williams M, Shu S, Plott C, Barry K, Rajasekar S, Grimwood J, Han X, Sun S, Hou Z, He W, Dai G, Sun C, Schmutz J, Leebens-Mack JH, Li FW, and Wang L
- Subjects
- Genome Size, Phylogeny, Evolution, Molecular, Genome, Plant genetics, Genomics
- Abstract
Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes ( Selaginella and Isoetes ) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum . Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species., Competing Interests: Competing interests statement:The authors declare no competing interest.
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- 2024
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14. Organellar phylogenomics of Ophioglossaceae fern genera.
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Kuo LY, Su HJ, Koubínová D, Xie PJ, Whitehouse C, Ebihara A, and Grant JR
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Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum . Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus , Helminthostachys, Mankyua , Sahashia , and Sceptridium . These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Kuo, Su, Koubínová, Xie, Whitehouse, Ebihara and Grant.)
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- 2024
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15. Unrecognised entrapment of a herniated bladder at the pubic symphysis following reduction and external fixation of an unstable pelvic fracture.
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Kuo LY, Silverman J, Morgan S, and Steer R
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- Humans, Male, External Fixators adverse effects, Fracture Fixation adverse effects, Fracture Fixation, Internal adverse effects, Fractures, Bone complications, Fractures, Bone diagnostic imaging, Fractures, Bone surgery, Fractures, Compression, Pelvic Bones injuries, Pelvic Bones surgery, Pubic Symphysis diagnostic imaging, Urinary Bladder diagnostic imaging, Urinary Bladder injuries, Urinary Bladder surgery
- Abstract
Bladder injury is frequently associated with complex pelvic fractures with men being the predominant population to sustain such injuries. Entrapment of the bladder through the site of pelvic fracture is a rare clinical entity. We report a case of an entrapped bladder post closed reduction and external fixation of an unstable anteroposterior compression type 3 (APC-3) fracture. This report highlights the diagnostic difficulty with identifying an entrapped bladder and the patient's functional outcome after 1 year of follow-up., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Limited 2023. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2023
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16. Effects of a prenatal mindfulness program on longitudinal changes in stress, anxiety, depression, and mother-infant bonding of women with a tendency to perinatal mood and anxiety disorder: a randomized controlled trial.
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Pan WL, Lin LC, Kuo LY, Chiu MJ, and Ling PY
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- Pregnancy, Female, Humans, Infant, Depression prevention & control, Depression psychology, Anxiety prevention & control, Anxiety diagnosis, Anxiety Disorders prevention & control, Stress, Psychological prevention & control, Stress, Psychological psychology, Mothers psychology, Mindfulness methods
- Abstract
Background: Stress is a risk factor for poor physical and mental health, affecting new mothers' ability, especially those with perinatal mood and anxiety disorders, to maintain their everyday lives. Over the past 50 years, global incidences of depression and anxiety disorders have increased, reaching pandemic levels. These incidences represent major public health issues that are challenging to detect and treat. Mindfulness programs are viable for reducing stress, anxiety, and depression. The present study evaluates mindfulness intervention effects on stress, anxiety, depression, and mother-infant bonding., Methods: We collected data on 102 women participating in a prenatal mindfulness program between July 2021 and March 2022; they were parallel and randomly assigned to experimental or control groups. The intervention group received an 8-week course in a prenatal mindfulness program, and the control group received usual standard prenatal care. The self-reported stress, pregnancy-related anxiety, and depression were assessed before and after the intervention and at 36 weeks of gestation. At 2 and 4 months postpartum, all participants provided self-reported their levels of stress, depression, and quality of mother-infant bonding., Results: Compared to the control group, the experimental group that received the prenatal mindfulness intervention experienced reduced prenatal stress, anxiety, and depression and reduced postnatal stress and depression. Despite this, there was no significant difference between the groups in terms of the quality of mother-infant bonding., Conclusions: Mindfulness prenatal programs are convenient and effective methods of decreasing stress, anxiety, and depression during the perinatal period. Based on our findings, prenatal mindfulness may play a role in mitigating mood and anxiety disorders and should be considered in future approaches to preventing psychological distress., Trial Registration Number: This trial has been prospectively registered at ClinicalTrials.gov (NCT04693130) and the first registration date was 12/24/2020., (© 2023. The Author(s).)
- Published
- 2023
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17. Modified CTAB protocols for high-molecular-weight DNA extractions from ferns.
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Xie PJ, Ke YT, and Kuo LY
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Premise: Efficient protocols for extracting high-molecular-weight (HMW) DNA from ferns facilitate the long-read sequencing of their large and complex genomes. Here, we perform two cetyltrimethylammonium bromide (CTAB)-based protocols to extract HMW DNA and evaluate their applicability in diverse fern taxa for the first time., Methods and Results: We describe two modified CTAB protocols, with key adjustments to minimize mechanical disruption during lysis to prevent DNA shearing. One of these protocols uses a small amount of fresh tissue but yields a considerable quantity of HMW DNA with high efficiency. The other accommodates a large amount of input tissue, adopts an initial step of nuclei isolation, and thus ensures a high yield in a short period of time. Both methods were proven to be robust and effective in obtaining HMW DNA from diverse fern lineages, including 33 species in 19 families. The DNA extractions mostly had high DNA integrity, with mean sizes larger than 50 kbp, as well as high purity (A
260 /A230 and A260 /A280 > 1.8)., Conclusions: This study provides HMW DNA extraction protocols for ferns in the hope of facilitating further attempts to sequence their genomes, which will bridge our genomic understanding of land plant diversity., (© 2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)- Published
- 2023
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18. Analyses of Marsilea vestita genome and transcriptomes do not support widespread intron retention during spermatogenesis.
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Rahmatpour N, Kuo LY, Kang J, Herman E, Lei L, Li M, Srinivasan S, Zipper R, Wolniak SM, Delwiche CF, Mount S, and Li FW
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- Animals, Introns genetics, Spermatogenesis genetics, Transcriptome genetics, Marsileaceae genetics
- Published
- 2023
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19. Editorial: Biology, systematics, and evolution of ferns and lycophytes in the omics era.
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Salino A, Rouhan G, Kuo LY, and Almeida TE
- Abstract
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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- 2023
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20. Thermal Recovery of the Electrochemically Degraded LiCoO 2 /Li 7 La 3 Zr 2 O 12 :Al,Ta Interface in an All-Solid-State Lithium Battery.
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Ihrig M, Kuo LY, Lobe S, Laptev AM, Lin CA, Tu CH, Ye R, Kaghazchi P, Cressa L, Eswara S, Lin SK, Guillon O, Fattakhova-Rohlfing D, and Finsterbusch M
- Abstract
All-solid-state lithium batteries are promising candidates for next-generation energy storage systems. Their performance critically depends on the capacity and cycling stability of the cathodic layer. Cells with a garnet Li
7 La3 Zr2 O12 (LLZO) electrolyte can show high areal storage capacity. However, they commonly suffer from performance degradation during cycling. For fully inorganic cells based on LiCoO2 (LCO) as cathode active material and LLZO, the electrochemically induced interface amorphization has been identified as an origin of the performance degradation. This study shows that the amorphized interface can be recrystallized by thermal recovery (annealing) with nearly full restoration of the cell performance. The structural and chemical changes at the LCO/LLZO heterointerface associated with degradation and recovery were analyzed in detail and justified by thermodynamic modeling. Based on this comprehensive understanding, this work demonstrates a facile way to recover more than 80% of the initial storage capacity through a thermal recovery (annealing) step. The thermal recovery can be potentially used for cost-efficient recycling of ceramic all-solid-state batteries.- Published
- 2023
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21. Fern Spores-"Ready-to-Use" Standards for Plant Genome Size Estimation Using a Flow Cytometric Approach.
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Tang SK, Lee PH, Liou WT, Lin CH, Huang YM, and Kuo LY
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Spores and pollen of plants were used as flow cytometric materials to efficiently infer genome sizes. Given this advantage, they hold great potential for various flow cytometric applications, particularly as plant genome size standards. To develop such novel standards, we investigated conditions of pretreatment (bead vortex), buffer, and reliable genome sizes of three fern spore collections- Cibotium taiwanense " Kuo4395 ", Sphaeropteris lepifera " Tang0001 ", and Alsophila metteniana " Lee s.n. ". Additionally, up to 30 year-old spore collections were obtained from herbarium specimens and from samples stored at 4 °C; their spore nuclei were extracted, and the quality and quantity of these nucleus extractions through storage ages were examined. Nuclear extractions with a longer bead vortex duration or lower spore/bead ratio generally resulted in a higher recovered quantity but a lower quality or purity. For each spore standard, the protocol optimization was determined by their performance in bead vortex conditions, and a 1C genome size was further inferred by linear regression ( C. taiwanense " Kuo4395 " = 5.058 pg; S. lepifera " Tang0001 " = 7.117 pg; and A. metteniana " Lee s.n. " = 19.379 pg). Spore nucleus quality and quantity are significantly negatively correlated with storage ages. Nuclear extractions of 10-year-old refrigerated spores remained qualified as a genome size standard; however, none of the herbarium spore collections fit such criteria. Our study is the first to develop and apply dried and refrigerated spores for genome size standards. These standards are ready to use, easy to manipulate, and feature long-term storage in comparison with traditionally used standards of fresh leaves.
- Published
- 2022
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22. Plastome phylogenomic analysis reveals evolutionary divergences of Polypodiales suborder Dennstaedtiineae.
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Lu JM, Du XY, Kuo LY, Ebihara A, Perrie LR, Zuo ZY, Shang H, Chang YH, and Li DZ
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- Bayes Theorem, Ferns classification, Ferns genetics, Species Specificity, Phylogeny
- Abstract
Background: Polypodiales suborder Dennstaedtiineae contain a single family Dennstaedtiaceae, eleven genera, and about 270 species, and include some groups that were previously placed in Dennstaedtiaceae, Hypolepidaceae, Monachosoraceae, and Pteridaceae. The classification and phylogenetic relationships among these eleven genera have been poorly understood. To explore the deep relationships within suborder Dennstaedtiineae and estimate the early diversification of this morphologically heterogeneous group, we analyzed complete plastomes of 57 samples representing all eleven genera of suborder Dennstaedtiineae using maximum likelihood and Bayesian inference., Results: The phylogenetic relationships of all the lineages in the bracken fern family Dennstaedtiaceae were well resolved with strong support values. All six genera of Hypolepidoideae were recovered as forming a monophyletic group with full support, and Pteridium was fully supported as sister to all the other genera in Hypolepidoideae. Dennstaedtioideae (Dennstaedtia s.l.) fell into four clades with full support: the Microlepia clade, the northern Dennstaedtia clade, the Dennstaedtia globulifera clade, and the Dennstaedtia s.s. clade. Monachosorum was strongly resolved as sister to all the remaining genera of suborder Dennstaedtiineae. Based on the well resolved relationships among genera, the divergence between Monachosorum and other groups of suborder Dennstaedtiineae was estimated to have occurred in the Early Cretaceous, and all extant genera (and clades) in Dennstaedtiineae, were inferred to have diversified since the Late Oligocene., Conclusion: This study supports reinstating a previously published family Monachosoraceae as a segregate from Dennstaedtiaceae, based on unique morphological evidence, the shady habitat, and the deep evolutionary divergence from its closest relatives., (© 2022. The Author(s).)
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- 2022
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23. Hymenophyllumchamaecyparicola (Hymenophyllaceae), a new filmy fern species from Taiwan.
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Chang ZX, Hsu TC, and Kuo LY
- Abstract
Hymenophyllumchamaecyparicola T.C.Hsu & Z.X.Chang, a new filmy fern species (Hymenophyllaceae) has been described from Taiwan and illustrated based on morphological and phylogenetic evidence. Although the new species resembles members in the subgenus Mecodium, namely H.wrightii , our plastid phylogeny has revealed that it is genetically distant from H.wrightii and forms a clade nested within subg. Hymenophyllum. The most notable characteristic to differentiate H.chamaecyparicola from related species is the presence of minute spathulate hairs on the surface of the rachis and veins. Hymenophyllumchamaecyparicola is currently only known from a small area in northern Taiwan, and endemic to that country., (Zhi-Xiang Chang, Tian-Chuan Hsu, Li-Yaung Kuo.)
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- 2022
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24. Systematics and Plastome Evolution in Schizaeaceae.
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Ke BF, Wang GJ, Labiak PH, Rouhan G, Chen CW, Shepherd LD, Ohlsen DJ, Renner MAM, Karol KG, Li FW, and Kuo LY
- Abstract
While the family Schizaeaceae (Schizaeales) represents only about 0.4% of the extant fern species diversity, it differs from other ferns greatly in gross morphologies, niche preferences, and life histories. One of the most notable features in this family is its mycoheterotrophic life style in the gametophytic stage, which appears to be associated with extensive losses of plastid genes. However, the limited number of sequenced plastomes, and the lack of a well-resolved phylogenetic framework of Schizaeaceae, makes it difficult to gain any further insight. Here, with a comprehensive sampling of ~77% of the species diversity of this family, we first inferred a plastid phylogeny of Schizaeaceae using three DNA regions. To resolve the deep relationships within this family, we then reconstructed a plastome-based phylogeny focusing on a selection of representatives that covered all the major clades. From this phylogenomic backbone, we traced the evolutionary histories of plastid genes and examined whether gene losses were associated with the evolution of gametophytic mycoheterotrophy. Our results reveal that extant Schizaeaceae is comprised of four major clades- Microschizaea , Actinostachys , Schizaea , and Schizaea pusilla . The loss of all plastid NADH-like dehydrogenase ( ndh ) genes was confirmed to have occurred in the ancestor of extant Schizaeaceae, which coincides with the evolution of mycoheterotrophy in this family. For chlorophyll biosynthesis genes ( chl ), the losses were interpreted as convergent in Schizaeaceae, and found not only in Actinostachys , a clade producing achlorophyllous gametophytes, but also in S. pusilla with chlorophyllous gametophytes. In addition, we discovered a previously undescribed but phylogenetically distinct species hidden in the Schizaea dichotoma complex and provided a taxonomic treatment and morphological diagnostics for this new species- Schizaea medusa . Finally, our phylogenetic results suggest that the current PPG I circumscription of Schizaea is non-monophyletic, and we therefore proposed a three-genus classification moving a subset of Schizaea species sensu PPG I to a third genus- Microschizaea ., Competing Interests: G-JW and MR were employed by Taiwan Semiconductor Manufacturing Company and Wildland Consultants. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ke, Wang, Labiak, Rouhan, Chen, Shepherd, Ohlsen, Renner, Karol, Li and Kuo.)
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- 2022
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25. Combining a transosseous cerclage wire after patellar tendon reattachment to treat patella distal pole fracture did not improve functional outcome.
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Kuo LY, Chen CY, and Lin KC
- Subjects
- Bone Wires, Humans, Patella surgery, Range of Motion, Articular, Retrospective Studies, Treatment Outcome, Fractures, Bone surgery, Knee Injuries surgery, Patellar Ligament surgery
- Abstract
This study aims to investigate whether an augmented wire in the treatment of patella distal pole fracture could improve knee range of motion (ROM) and radiographic features. Thirty-five consecutive patients with patellar distal pole fracture were analyzed from January 2014 to July 2019. The treatment is divided into two groups according to the presence or absence of augmented wire. Knee ROM, bone union, extension lag, and patellar height were compared between these two groups as the clinical and radiological outcomes. There was no significant difference in mean knee ROM (110° vs. 108°, p = 0.79), proportion of patella baja or bone union. More extension lag was noted in the augmentation group (5/20, 25%) than in the tendon reattachment group (1/15, 6.7%) with no statistically significant difference. In the augmentation group, four cases (20%) would need to remove the fixator due to irritation or broken hardware. Maintaining the patella length by preserving the distal pole and repairing the torn retinaculum allowed early motion to avoid knee stiffness safely without augmentation wire, which doesn't improve knee ROM. The patellar tendon reattachment alone could achieve a great recovery and prevent the need for a second surgery due to broken wire or irritation., (© 2022. The Author(s).)
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- 2022
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26. Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns.
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Du XY, Kuo LY, Zuo ZY, Li DZ, and Lu JM
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Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns were sampled, making it the most comprehensive plastomic analysis of fern lineages to date. The samples included 42 novel plastomes of 15 families with a focus on Hymenophyllales and Gleicheniales. We reconstructed a well-supported phylogeny of all extant fern families, detected significant structural synapomorphies, including 9 large inversions, 7 invert repeat region (IR) boundary shifts, 10 protein-coding gene losses, 7 tRNA gene losses or anticodon changes, and 19 codon indels (insertions or deletions) across the deep phylogeny of ferns, particularly on the backbone nodes. The newly identified inversion V5, together with the newly inferred expansion of the IR boundary R5, can be identified as a synapomorphy of a clade composed of Dipteridaceae, Matoniaceae, Schizaeales, and the core leptosporangiates, while a unique inversion V4, together with an expansion of the IR boundary R4, was verified as a synapomorphy of Gleicheniaceae. This structural evidence is in support of our phylogenetic inference, thus providing key insight into the paraphyly of Gleicheniales. The inversions of V5 and V7 together filled the crucial gap regarding how the "reversed" gene orientation in the IR region characterized by most extant ferns (Schizaeales and the core leptosporangiates) evolved from the inferred ancestral type as retained in Equisetales and Osmundales. The tRNA genes trnR-ACG and trnM-CAU were assumed to be relicts of the early-divergent fern lineages but intact in most Polypodiales, particularly in eupolypods; and the loss of the tRNA genes trnR-CCG, trnV-UAC , and trnR-UCU in fern plastomes was much more prevalent than previously thought. We also identified several codon indels in protein-coding genes within the core leptosporangiates, which may be identified as synapomorphies of specific families or higher ranks. This study provides an empirical case of integrating structural and sequence information of plastomes to resolve deep phylogeny of plants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Du, Kuo, Zuo, Li and Lu.)
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- 2022
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27. The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence.
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Huang X, Wang W, Gong T, Wickell D, Kuo LY, Zhang X, Wen J, Kim H, Lu F, Zhao H, Chen S, Li H, Wu W, Yu C, Chen S, Fan W, Chen S, Bao X, Li L, Zhang D, Jiang L, Khadka D, Yan X, Liao Z, Zhou G, Guo Y, Ralph J, Sederoff RR, Wei H, Zhu P, Li FW, Ming R, and Li Q
- Subjects
- Animals, Genome, Plant, Phylogeny, Atelinae genetics, Ferns genetics, Spiders genetics
- Abstract
To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology., (© 2022. The Author(s).)
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- 2022
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28. Providing the missing links in fern life history: Insights from a phenological survey of the gametophyte stage.
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Quinlan A, Lee PH, Tang TY, Huang YM, Chiou WL, and Kuo LY
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Premise: The entire life cycle of ferns has been documented, yet their life histories are still poorly understood. In particular, the phenology of fern gametophytes remains largely unknown. To address this issue, we demonstrated a new ecological approach to explore the phenological link between spore release and gametophyte maturation within the life history of a tree fern species., Methods: We conducted a serial survey of Alsophila podophylla gametophyte abundance in the field, and recorded the time of its spore release. Every two months for one year, all terrestrial fern gametophytes in an unsampled subplot were collected and identified using tissue-direct PCR., Results: We found temporal differences in gametophyte abundances, with a sevenfold difference between the highest and lowest months. The number of spores released was linked to the gametophyte abundance two months later. The switch from gametophyte to juvenile sporophyte was found to be most correlated with precipitation., Discussion: The observed fluctuation in gametophyte abundance and population structure was likely associated with the phenology of spore release and environmental factors. Importantly, these findings provide the first evidence of phenological links between different developmental stages in a fern's life history., (© 2022 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2022
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29. Integrating tissue-direct PCR into genetic identification: An upgraded molecular ecology approach to survey fern gametophytes in the field.
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Wu YH, Ke YT, Chan YY, Wang GJ, and Kuo LY
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Premise: The gametophytes of different fern species collected in the field can be difficult to distinguish because of their morphological similarities. Nonetheless, emerging molecular ecology techniques are starting to be used to tackle such limitations. Here, using case studies and a detailed protocol, we demonstrate a convenient methodology, tissue-direct PCR (TD-PCR), that foregoes a traditional DNA extraction and facilitates the identification of fern gametophytes, as well as enabling the elucidation of their natural distribution., Methods: Based on updated plastome information, we designed a universal primer set targeting the trnL-L-F region, which is effective across extant ferns. We used this primer set to perform TD-PCR on the case-studied populations of Taiwanese Lomariopsis gametophytes, using the generated sequences for their identification. In the case study concerning the microhabitat preference of Vaginularia junghuhnii , we designed and used a taxon-specific primer set., Results: Compared with approaches requiring DNA extraction, the use of TD-PCR with either universal or taxon-specific primers could save significant time, money, labor, and research materials in the genetic identification of fern gametophytes., Discussion: The use of modern genetic tools can aid in the identification of fern gametophytes. An updated TD-PCR strategy not only facilitates the DNA-based identification of gametophytes, but also promotes new avenues of research for investigating these plants in the field., (© 2022 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2022
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30. Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques.
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Chen KH, Xie QY, Chang CC, and Kuo LY
- Abstract
Premise: Several ferns and lycophytes produce subterranean gametophytes, including the Ophioglossaceae, Psilotaceae, and some members of the Schizaeaceae, Gleicheniaceae, and Lycopodiaceae. Despite the surge in plant-microbiome research, which has been particularly boosted by high-throughput sequencing techniques, the microbiomes of these inconspicuous fern gametophytes have rarely been examined. The subterranean gametophytes are peculiar due to their achlorophyllous nature, which makes them rely on fungi to obtain nutrients. Furthermore, the factors that shape the fungal communities (mycobiomes) of fern gametophytes have not been examined in depth., Methods and Results: We present a workflow to study the mycobiome of the achlorophyllous gametophytes of Ophioderma pendulum using a high-throughput metabarcoding approach. Simultaneously, each gametophyte was investigated microscopically to detect fungal structures. Two primer sets of the nuclear ITS sequence targeting general fungi were applied, in addition to a primer set that specifically targets the nuclear small subunit ribosomal rDNA region of arbuscular mycorrhizal fungi. Both the microscopic and metabarcoding approaches revealed many diverse fungi inhabiting a single gametophyte of O . pendulum ., Discussion: This study provides methodological details and discusses precautions for the mycobiome investigation of achlorophyllous gametophytes. This research is also the first to uncover the mycobiome assembly of an achlorophyllous gametophyte of an epiphytic fern., (© 2022 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2022
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31. Study of LiCoO 2 /Li 7 La 3 Zr 2 O 12 :Ta Interface Degradation in All-Solid-State Lithium Batteries.
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Ihrig M, Finsterbusch M, Laptev AM, Tu CH, Tran NTT, Lin CA, Kuo LY, Ye R, Sohn YJ, Kaghazchi P, Lin SK, Fattakhova-Rohlfing D, and Guillon O
- Abstract
The garnet-type Li
7 La3 Zr2 O12 (LLZO) ceramic solid electrolyte combines high Li-ion conductivity at room temperature with high chemical stability. Several all-solid-state Li batteries featuring the LLZO electrolyte and the LiCoO2 (LCO) or LiCoO2 -LLZO composite cathode were demonstrated. However, all batteries exhibit rapid capacity fading during cycling, which is often attributed to the formation of cracks due to volume expansion and the contraction of LCO. Excluding the possibility of mechanical failure due to crack formation between the LiCoO2 /LLZO interface, a detailed investigation of the LiCoO2 /LLZO interface before and after cycling clearly demonstrated cation diffusion between LiCoO2 and the LLZO. This electrochemically driven cation diffusion during cycling causes the formation of an amorphous secondary phase interlayer with high impedance, leading to the observed capacity fading. Furthermore, thermodynamic analysis using density functional theory confirms the possibility of low- or non-conducting secondary phases forming during cycling and offers an additional explanation for the observed capacity fading. Understanding the presented degradation paves the way to increase the cycling stability of garnet-based all-solid-state Li batteries.- Published
- 2022
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32. Two new species in the fern genus Lomariopsis (Lomariopsidaceae) from East Asia.
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Wu YH, Sun CY, Ebihara A, Lu NT, Rouhan G, and Kuo LY
- Abstract
Two East Asian Lomariopsis (Lomariopsidaceae, Polypodiales) species, Lomariopsismoorei and Lomariopsislongini , which were previously misidentified as L.spectabilis , are here described as new species based on evidence from morphological characters and a molecular phylogeny. The two species differ from the three other described species in East Asia by their venation, pinna shapes, and perine morphology. A phylogeny based on a combined dataset of three chloroplast regions ( rbcL + rps4-trnS + trnL-L-F ) showed that L.moorei and L.longini each formed a well-supported monophyletic group which was distantly related to both L.spectabilis and the other morphologically similar East Asian species, L.boninensis ., (Yi-Hsuan Wu, Chih-Yun Sun, Atsushi Ebihara, Ngan Thi Lu, Germinal Rouhan, Li-Yaung Kuo.)
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- 2021
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33. A dormant resource for genome size estimation in ferns: C-value inference of the Ophioglossaceae using herbarium specimen spores.
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Kuo LY, Tang SK, Kao TT, Ebihara A, Fawcett S, Hsiao MC, Shinohara W, and Dauphin B
- Abstract
Premise: The great variation of genome size (C-value) across land plants is linked to various adaptative features. Flow cytometry (FCM), the standard approach to estimating C-values, relies mostly on fresh materials, performing poorly when used with herbarium materials. No fern C-value reports have been derived from herbarium specimens; however, the herbarium spores of some ferns remain highly viable for decades and are thus promising for further investigation. To explore this possibility, we evaluated herbarium spore collections of Ophioglossaceae ferns using FCM., Methods: Flow cytometry was conducted on 24 spore samples, representing eight of the 12 genera of the Ophioglossaceae, using specimens ranging in age from 2.6 to 111 years obtained from five herbaria., Results: Regardless of the genus or the source herbarium, high-quality C-value data were generated from 17 samples, with the oldest being 26 years old. Estimates of the C-values from sporophytic tissues of known ploidy did not reveal any evidence of apomixis for the species surveyed here. We also detected a pronounced genome downsizing in Sceptridium polyploids., Discussion: The recent success of FCM for C-value estimation using spores provides a much more convenient method of utilizing "dry" refrigerated materials. We demonstrate here that herbarium spores of some ferns are also promising for this use, even for older specimens., (© 2021 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
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- 2021
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34. Underwater CAM photosynthesis elucidated by Isoetes genome.
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Wickell D, Kuo LY, Yang HP, Dhabalia Ashok A, Irisarri I, Dadras A, de Vries S, de Vries J, Huang YM, Li Z, Barker MS, Hartwick NT, Michael TP, and Li FW
- Subjects
- Carbon Dioxide metabolism, Crassulacean Acid Metabolism genetics, Evolution, Molecular, Gene Expression, Genome, Genome Size, Lignin biosynthesis, Magnoliopsida, Plants metabolism, Taiwan, Water, Whole Genome Sequencing, Crassulacean Acid Metabolism physiology, Photosynthesis physiology, Tracheophyta genetics, Tracheophyta metabolism
- Abstract
To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO
2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known 'bacterial-type' PEPC, along with the 'plant-type' exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized., (© 2021. The Author(s).)- Published
- 2021
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35. Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic.
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Du XY, Lu JM, Zhang LB, Wen J, Kuo LY, Mynssen CM, Schneider H, and Li DZ
- Subjects
- Animals, Bayes Theorem, Biodiversity, Biological Evolution, Ferns, Fossils, Magnoliopsida classification, Magnoliopsida genetics, Phylogeny
- Abstract
Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints reflecting current interpretations of fossil record. Our plastome phylogeny recovered the same six major lineages as a recent nuclear phylogeny, but the position of Dennstaedtiineae was different. The present phylogeny showed high resolution of relationships among the families of Polypodiales, especially among those forming the Aspleniineae. The divergence time estimates supported the most recent common ancestor of Polypodiales and its closest relative dating back to the Triassic, establishment of the major lineages in the Jurassic, and a likely accelerated radiation during the late Jurassic and the Early Cretaceous. The estimated divergence patterns of Polypodiales and angiosperms converge to a scenario in which their main lineages were established simultaneously shortly before the onset of the Cretaceous Terrestrial Revolution, and further suggest a pre-Cretaceous hidden history for both lineages. The pattern of simultaneous diversifications shown here elucidate an important gap in our understanding of the Terrestrial Revolution that shaped today's ecosystems., (© 2021 Willi Hennig Society.)
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- 2021
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36. Sulfide Oxidation by 2,6-Bis[hydroxyl(methyl)amino]-4-morpholino-1,3,5-triazinatodioxomolybdenum(VI): Mechanistic Implications with DFT Calculations for a New Class of Molybdenum(VI) Complex.
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Bullock CX, Jamieson CS, Moënne-Loccoz P, Taylor B, Gonzalez JAM, Draves EA, and Kuo LY
- Abstract
Sulfide oxidation is accomplished by a new class of dioxomolybdenum(VI) catalyst ( 1 ) that uses the tridentate 2,6-bis[hydroxyl(methyl)amino]-4-morpholino-1,3,5-triazine ligand to form a five-coordinate molybdenum(VI) center. Resonance Raman spectra show that the dioxo groups on the Mo(VI) oxygens readily exchange with water in an acetonitrile media that allows
18 O labeling of catalyst 1 . The model oxidation reaction was the conversion of thioanisole ( 2 ) to the corresponding sulfoxide with 4% of 1 using an equimolar amount of H2 O2 in MeCN- d3 . Oxygen-18 labeling experiments with either18 O-labeled 1 or18 O-labeled H2 O2 are consistent with a sulfide oxygenation pathway that uses a η1 -Mo(OOH) hydroxoperoxyl species ( 3 ). The hypothesized intermediate 3 is initially formed in a proton transfer reaction between 1 and H2 O2 . Oxidation is hypothesized via nucleophilic attack of the sulfide on 3 that is supported from a Hammett linear free-energy relationship for para-derivatives of 2 . A Hammett reactivity constant (ρ) of -1.2 ± 0.2 was obtained, which is consistent with other ρ values found in prior sulfide oxidation reactions by group 6 complexes. An Eyring plot of the 2 oxidation by 1 gives an Ea of 63.0 ± 5.2 kJ/mol, which is slightly higher than that of a similar oxidation of 2 by the molybdenum(VI) complex, oxodiperoxo (pyridine-2-carboxylato)molybdate(VI) bis(pyridine-2-carboxylic acid) monohydrate ( 5 ). Computational modeling with density functional theory (DFT) of the complete reaction profile gave enthalpy and entropy of activations (64 kJ/mol and -120 J/mol·K, respectively) within 1 standard deviation of the experimental values, further supporting the hypothesized mechanism.- Published
- 2021
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37. Synthesis, biological evaluation, and correlation of cytotoxicity versus redox potential of 1,4-naphthoquinone derivatives.
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Shen CC, Afraj SN, Hung CC, Barve BD, Kuo LY, Lin ZH, Ho HO, and Kuo YH
- Subjects
- Antineoplastic Agents chemical synthesis, Antineoplastic Agents chemistry, Cell Proliferation drug effects, Dose-Response Relationship, Drug, Drug Screening Assays, Antitumor, HeLa Cells, Humans, KB Cells, Molecular Structure, Naphthoquinones chemical synthesis, Naphthoquinones chemistry, Oxidation-Reduction, Structure-Activity Relationship, Topoisomerase I Inhibitors chemical synthesis, Topoisomerase I Inhibitors chemistry, Antineoplastic Agents pharmacology, DNA Topoisomerases, Type I metabolism, Naphthoquinones pharmacology, Topoisomerase I Inhibitors pharmacology
- Abstract
A series of 1,4-naphthoquinone derivatives of lawsone (1), 6-hydroxy-1,4-naphthoquinone (2), and juglone (3) were synthesized by alkylation, acylation, and sulfonylation reactions. The yields of lawsone derivatives 1a-1k (type A), 6-hydroxy-1,4-naphthoquinone derivatives 2a-2j (type B), and juglone derivatives 3a-3h (type C) were 52-99%, 53-96%, and 28-95%, respectively. All compounds were tested in vitro for the cytotoxicity against human oral epidermoid carcinoma (KB) and cervix epithelioid carcinoma (HeLa) cells and their structure-activity relationship was studied. Compound 3c was found to be most potent in KB cell line (IC
50 = 1.39 µM). Some compounds were evaluated for DNA topoisomerase I inhibition. Compounds 2c, 3, 3a, and 3d showed topoisomerase inhibition activity with IC50 values of 8.3-91 µM. Standard redox potentials (E°) of all naphthoquinones in phosphate buffer at pH 7.2 were examined by means of cyclic voltammetry. A definite correlation has been found between the redox potentials and inhibitory effects of type A compounds., (Copyright © 2021 Elsevier Ltd. All rights reserved.)- Published
- 2021
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38. The incidence of mental disorder increases after hip fracture in older people: a nationwide cohort study.
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Kuo LY, Hsu PT, Wu WT, Lee RP, Wang JH, Chen HW, Chen IH, Yu TC, Peng CH, Liu KL, Hsu CY, and Yeh KT
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- Aged, Aged, 80 and over, Cohort Studies, Humans, Incidence, Proportional Hazards Models, Retrospective Studies, Risk Factors, Taiwan epidemiology, Hip Fractures diagnosis, Hip Fractures epidemiology
- Abstract
Background: People living with dementia seem to be more likely to experience delirium following hip fracture. The association between mental disorders (MD) and hip fracture remains controversial. We conducted a nationwide study to examine the prevalence of MD in geriatric patients with hip fractures undergoing surgery and conducted a related risk factor analysis., Material and Methods: This retrospective cohort study used data from Taiwan's National Health Insurance Research Database between 2000 and 2012 and focused on people who were older than 60 years. Patients with hip fracture undergoing surgical intervention and without hip fracture were matched at a ratio of 1:1 for age, sex, comorbidities, and index year. The incidence and hazard ratios of age, sex, and multiple comorbidities related to MD and its subgroups were calculated using Cox proportional hazards regression models., Results: A total of 1408 patients in the hip fracture group and a total of 1408 patients in the control group (no fracture) were included. The overall incidence of MD for the hip fracture and control groups per 100 person-years were 0.8 and 0.5, respectively. Among MD, the incidences of transient MD, depression, and dementia were significantly higher in the hip fracture group than in the control group., Conclusions: The prevalence of newly developed MD, especially transient MD, depression, and dementia, was higher in the geriatric patients with hip fracture undergoing surgery than that in the control group. Prompt and aggressive prevention protocols and persistent follow-up of MD development is highly necessary in this aged society.
- Published
- 2021
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39. Major adverse cardiac events and functional capacity in patients at intermediate risk undergoing transcatheter versus surgical aortic valve replacement for aortic stenosis with bicuspid valves.
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Tsai HY, Lin YS, Wu IC, Kuo LY, Chen BY, Shen SL, Hsu WN, and Huang HY
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- Adult, Aged, Aged, 80 and over, Aortic Valve surgery, Humans, Middle Aged, Mitral Valve, Risk Assessment, Risk Factors, Treatment Outcome, Aortic Valve Stenosis complications, Aortic Valve Stenosis surgery, Heart Valve Prosthesis Implantation, Transcatheter Aortic Valve Replacement
- Abstract
Background: Transcatheter aortic valve replacement (TAVR) is not always the optimal option for aortic valve stenosis (AS) patients with bicuspid aortic valves (BcAVs) and many studies exclude this group of patients. The aim of our study was to compare the rate of a major adverse cardiovascular event (MACE) and functional capacity in AS patients with BcAV after surgical aortic valve replacement (SAVR) and TAVR., Methods: This study included 130 patients who underwent SAVR or TAVR from July 2013 to August 2018 at the Cheng Hsin General Hospital. The main outcome was MACE. Events recorded included noncardiovascular (CV) mortality, CV mortality, recurrent nonfatal stroke, recurrent nonfatal myocardial infarction (MI), and important events. The secondary outcome was functional recovery, which was defined according to the metabolic equivalent (MET) 6 months after the aortic procedure., Results: The mean age of patients was 56.8 ± 26.9 years and the mean Society of Thoracic Surgeons score was 3.29 ± 4.69. Logistic regression analyses indicated that SAVR was a significant predictor of functional recovery. Patients who underwent SAVR had a higher rate of functional recovery (>3 METs; 87.8%, p = .000) and had a significantly higher odds ratio (3.56; 95% confidence interval, 1.19-10.63, p = .023). The Kaplan-Meier survival analysis showed that the MACE rate was not associated with the aortic procedure., Conclusions: Our analysis showed that SAVR is a significant predictor of better functional recovery and TAVR is associated with a lower level of functional capacity. In summary, TAVR is an acceptable option for AS patients with BcAV, and for a better prognosis, an early intervention aimed at improving functional capacity is highly recommended for this group of patients., (© 2021 Wiley Periodicals LLC.)
- Published
- 2021
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40. A global phylogeny of Stegnogramma ferns (Thelypteridaceae): generic and sectional revision, historical biogeography and evolution of leaf architecture.
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Kuo LY, Chang YH, Huang YH, Testo W, Ebihara A, Rouhan G, Quintanilla LG, Watkins JE Jr, Huang YM, and Li FW
- Abstract
The thelypteroid fern genus Stegnogramma s.l. contains around 18-35 species and has a global, cross-continental distribution ranging from tropical to temperate regions. Several genera and infrageneric sections have been recognized previously in Stegnogramma s.l., but their phylogenetic relationships are still unclear. In this study, we present a global phylogeny of Stegnogramma s.l. with the most comprehensive sampling to date and aim to pinpoint the phylogenetic positions of biogeographically and taxonomically important taxa. Based on the reconstructed historical biogeography and character evolution, we propose a new (infra)generic classification and discuss the diversification of Stegnogramma s.l. in a biogeographical context. New names or combinations are made for 12 (infra)species, including transferring the monotypic species of Craspedosorus to Leptogramma. Finally, we discuss a possible link between leaf architecture and ecological adaptation, and hypothesize that the increase in leaf dissection and free-vein proportion is an adaptive feature to cool climates in Stegnogramma s.l., (© The Willi Hennig Society 2019.)
- Published
- 2020
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41. Predicting exercise capacity recovery immediately after mitral valve surgery.
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Lin YS, Lin WH, Tsai HY, Huang HY, Kuo LY, and Chen BY
- Subjects
- Aged, Aged, 80 and over, Exercise Test, Female, Follow-Up Studies, Humans, Male, Middle Aged, Postoperative Period, Prognosis, Retrospective Studies, Exercise Tolerance physiology, Heart Valve Prosthesis Implantation methods, Mitral Valve surgery, Mitral Valve Insufficiency surgery, Recovery of Function physiology
- Abstract
Background: This study presents the exercise capacity of postmitral valve surgery patients and determines predictors capable of affecting recovery., Methods: A total of 302 patients with mitral regurgitation who had undergone mitral surgery at the Heart Center in Taiwan from 1 August 2013 to 31 December 2015 were included in the present study. Data related to specific predictors of operative outcome were collected, including demographic data, intraoperative factors, exercise tolerance, echocardiogram data, concurrent cardiovascular disease history, comorbidities, lifestyle risk factors, and surgery types. Postoperative exercise capacity was presented as peak oxygen consumption (VO
2 ; mL of O2 /kg/min) determined by exercise tests 3 weeks after surgery. Subjects were separated into two groups: a preserved recovery (peak VO2 ≥ 65% of predicted VO2max ) group and a poor recovery group (peak VO2 < 65% of predicted VO2max ). Preliminary univariate analysis was performed to test for possible relationships between predictive variables and exercise capacity. An analysis of all items shown to be significantly different between the two groups was then subjected to multivariate logistic regression analysis. Detected differences with P < .05 were considered significant., Results: Among the 302 patients sampled, female sex (odds ratio [OR], 2.65; 95% confidence interval [95% CI], 1.58-4.47), obesity (OR, 0.26; 95% CI, 0.10-0.64), sedentary lifestyle (OR, 0.47; 95% CI, 0.28-0.79), and high preoperative New York Heart Association Functional Classification level (OR, 0.52; 95% CI, 0.31-0.87) were significant predictors of poor exercise capacity., Conclusions: Without complicated clinical procedures, physicians and medical teams could easily use these items of information to screen the exercise capacity of mitral valve surgery patients and prepare a suitable after surgery plan if needed or request a consultation as early as possible., (© 2019 Wiley Periodicals, Inc.)- Published
- 2019
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42. Promoting the Transformation of Li 2 S 2 to Li 2 S: Significantly Increasing Utilization of Active Materials for High-Sulfur-Loading Li-S Batteries.
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Yang X, Gao X, Sun Q, Jand SP, Yu Y, Zhao Y, Li X, Adair K, Kuo LY, Rohrer J, Liang J, Lin X, Banis MN, Hu Y, Zhang H, Li X, Li R, Zhang H, Kaghazchi P, Sham TK, and Sun X
- Abstract
Lithium-sulfur (Li-S) batteries with high sulfur loading are urgently required in order to take advantage of their high theoretical energy density. Ether-based Li-S batteries involve sophisticated multistep solid-liquid-solid-solid electrochemical reaction mechanisms. Recently, studies on Li-S batteries have widely focused on the initial solid (sulfur)-liquid (soluble polysulfide)-solid (Li
2 S2 ) conversion reactions, which contribute to the first 50% of the theoretical capacity of the Li-S batteries. Nonetheless, the sluggish kinetics of the solid-solid conversion from solid-state intermediate product Li2 S2 to the final discharge product Li2 S (corresponding to the last 50% of the theoretical capacity) leads to the premature end of discharge, resulting in low discharge capacity output and low sulfur utilization. To tackle the aforementioned issue, a catalyst of amorphous cobalt sulfide (CoS3 ) is proposed to decrease the dissociation energy of Li2 S2 and propel the electrochemical transformation of Li2 S2 to Li2 S. The CoS3 catalyst plays a critical role in improving the sulfur utilization, especially in high-loading sulfur cathodes (3-10 mg cm-2 ). Accordingly, the Li2 S/Li2 S2 ratio in the discharge products increased to 5.60/1 from 1/1.63 with CoS3 catalyst, resulting in a sulfur utilization increase of 20% (335 mAh g-1 ) compared to the counterpart sulfur electrode without CoS3 ., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)- Published
- 2019
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43. Unraveling the Role of Earth-Abundant Fe in the Suppression of Jahn-Teller Distortion of P'2-Type Na 2/3 MnO 2 : Experimental and Theoretical Studies.
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Choi JU, Park YJ, Jo JH, Kuo LY, Kaghazchi P, and Myung ST
- Abstract
Layered Na
2/3 MnO2 suffers from capacity loss due to Jahn-Teller (J-T) distortion by Mn3+ ions. Herein, density functional theory calculations suggest Na2/3 [Fex Mn1- x ]O2 suppresses the J-T effect. The Fe substitution results in a decreased oxygen-metal-oxygen length, leading to decreases in the b and c lattice parameters but an increase in the a lattice constant. As a result, the capacity retention and rate capability are enhanced with an additional redox pair associated with Fe4+/3+ . Finally, the thermal properties are improved, with the Fe substitution delaying the exothermic reaction and reducing exothermic heat.- Published
- 2018
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44. New Hirsutinolide-Type Sesquiterpenoids from Vernonia cinerea Inhibit Nitric Oxide Production in LPS-Stimulated RAW264.7 Cells.
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Kuo LY, Tseng PY, Lin YC, Liaw CC, Zhang LJ, Tsai KC, Lin ZH, Ho HO, and Kuo YH
- Subjects
- Animals, Anti-Inflammatory Agents, Non-Steroidal chemistry, Drug Evaluation, Preclinical methods, Inhibitory Concentration 50, Lipopolysaccharides pharmacology, Magnetic Resonance Spectroscopy, Mice, Molecular Structure, RAW 264.7 Cells, Spectrometry, Mass, Electrospray Ionization, Structure-Activity Relationship, Anti-Inflammatory Agents, Non-Steroidal pharmacology, Nitric Oxide biosynthesis, Sesquiterpenes chemistry, Sesquiterpenes pharmacology, Vernonia chemistry
- Abstract
Phytochemical investigation of ethanol extracts from two Taiwanese collections of Vernonia cinerea resulted in the isolation of eighteen hirsutinolide-type sesquiterpenoids, including seven new ones designated as vernolides E - K (1: -7: ). All structures were determined by a combination of detailed spectroscopic analyses (NMR and MS) and comparison with reported data. In an in vitro anti-inflammatory assay, compounds 3, 7, 9, 11: , and 14: exhibited strong inhibitory activities toward NO production by LPS-induced RAW264.7 macrophages, with IC
50 values of 1.18, 0.85, 0.66, 0.71 and 0.45 µM, respectively, without affecting cellular viability at 40 µM. Preliminary structure-activity relationships indicate that the ester groups at C-8 and C-13 may enhance inhibition of NO production., Competing Interests: The authors declare no conflict of interest., (Georg Thieme Verlag KG Stuttgart · New York.)- Published
- 2018
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45. VE/VCO 2 Slope and Functional Capacity in Patients Post-Heart Transplantation.
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Tsai WJ, Tsai HY, Kuo LY, Lin YS, Chen BY, Lin WH, Shen SL, and Huang HY
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- Aged, Cross-Sectional Studies, Exercise Test, Female, Humans, Male, Middle Aged, Multivariate Analysis, Oxygen Consumption, Prognosis, Respiratory Function Tests, Heart Failure diagnosis, Heart Failure physiopathology, Heart Transplantation, Pulmonary Ventilation physiology
- Abstract
Background: The ventilatory efficiency represented cardiovascular, pulmonary, and musculoskeletal performance into an integrate index has been used as long-term and short-term prognostic variables in congestive heart failure. The heart failure patients post heart transplantation, whether the ventilatory efficiency was also normalized is still unknown., Methods: This was a cross-sectional study. We measured ventilation to carbon dioxide production slope and oxygen consumption in peak exercise (peak VO
2 ) by cardiopulmonary exercise test, which represented ventilatory efficiency and functional capacity respectively. Strength of hand grip, the 30-second chair stand test, and 6-minute walking test were also evaluated. Patients with ventilation to carbon dioxide production slope <30 were defined as the normal group; others were defined as the abnormal group. Independent t tests and paired t tests were used when appropriate. The level of statistical significance was set at .05., Results: There were 51 clinically stable post-heart transplantation patients (age 53 ± 12.4 years; 86.3% were male) at 65.14 ± 41.17 months after transplantation. The ventilation to carbon dioxide production slope was 29.2 ± 5.6, which significantly improved compared to that recorded 1 month after heart transplantation (32.6 ± 6.4). There were 20 patients in the abnormal group, characterized by lower 6-minute walking test distance (normal vs abnormal, 422.5 ± 97.8 vs 532.6 ± 87.6 m) and peak VO2 (normal vs abnormal, 14.9 ± 5.3 vs 18.8 ± 5.1 mL/kg/min). The abnormal ventilation to carbon dioxide production slope was significantly correlated with 6-minute walking test distances in multivariate analyses., Conclusion: Our findings indicate that the ventilation to carbon dioxide production slope is partially abnormal among patients post-heart transplantation. A ventilation to carbon dioxide production slope above the normal range is characterized by a lower peak VO2 during cardiopulmonary exercise test and lower 6-minute walking test distance. The ventilation to carbon dioxide production slope is also significantly negatively correlated with peak VO2 , peak work rate, and 6-minute walking test distance. The prognostic utility of the ventilation to carbon dioxide production slope for patients post-heart transplantation requires further investigation., (Copyright © 2018 Elsevier Inc. All rights reserved.)- Published
- 2018
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46. Oxygen Consumption at Anaerobic Threshold Predicts Cardiac Events After Heart Transplantation.
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Tsai HY, Tsai WJ, Kuo LY, Lin YS, Chen BY, Lin WH, Shen SL, and Huang HY
- Subjects
- Adult, Aged, Cohort Studies, Exercise Test, Exercise Tolerance physiology, Female, Heart Failure diagnosis, Heart Failure mortality, Heart Transplantation mortality, Humans, Male, Middle Aged, Prognosis, Retrospective Studies, Anaerobic Threshold physiology, Heart Failure physiopathology, Heart Transplantation adverse effects
- Abstract
Objectives: The ventilatory efficiency and functional capacity measured by the cardiopulmonary exercise test (CPET) have been used as important prognostic variables in congestive heart failure. This study sought to identify whether these predictors before heart transplantation (HTX) play a key role in predicting adverse events in patients with heart failure after HTX., Methods: This was a retrospective cohort study design. HTX recipients were included for analysis. Ventilation to carbon dioxide production slope (VE/VCO
2 slope) and oxygen consumption (VO2 ) during exercise were collected by CPET, which represented ventilator efficiency and functional capacity respectively. Cardiac-related events 2 years after HTX were recorded by chart review. We divided patients into 2 groups based on VE/VCO2 slope = 34, peak VO2 = 14 mL/kg/min and VO2 at aerobic threshold (AT) = 11 mL/kg/min. Kaplan-Meier survival curves was used to represent the events rate between groups and Log rank test was used to test significance., Results: A total of 87 patients after HTX were included. Mean (SD) age was 48 (11) years and 73 were male; 28 subjects suffered from events, and 76 cardiac events were recorded. The mean (SD) data of peak VO2 , VO2 at AT, and VE/VCO2 slope analyzed from CPET were 17.8 (5.6) mL/kg/min, 15.4 (4.4) mL/kg/min, and 33.1 (8.2) mL/kg/min, respectively. Lower VO2 at AT contributed to increase events rate (P < .05)., Conclusion: Aerobic capacity may better predict 2-year cardiac events in patients after HTX. Strategies to improve aerobic capacity should be focused on in the cohort., (Copyright © 2018 Elsevier Inc. All rights reserved.)- Published
- 2018
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47. A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families.
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Qi X, Kuo LY, Guo C, Li H, Li Z, Qi J, Wang L, Hu Y, Xiang J, Zhang C, Guo J, Huang CH, and Ma H
- Subjects
- Evolution, Molecular, Fossils, Gene Duplication, Likelihood Functions, Time Factors, Transcription Factors genetics, Transcriptome genetics, Cell Nucleus genetics, Ferns classification, Ferns genetics, Phylogeny, Transcription Factors metabolism
- Abstract
Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns., (Copyright © 2018 Elsevier Inc. All rights reserved.)
- Published
- 2018
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48. Stabilizing the Interface of NASICON Solid Electrolyte against Li Metal with Atomic Layer Deposition.
- Author
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Liu Y, Sun Q, Zhao Y, Wang B, Kaghazchi P, Adair KR, Li R, Zhang C, Liu J, Kuo LY, Hu Y, Sham TK, Zhang L, Yang R, Lu S, Song X, and Sun X
- Abstract
Solid-state batteries have been considered as one of the most promising next-generation energy storage systems because of their high safety and energy density. Solid-state electrolytes are the key component of the solid-state battery, which exhibit high ionic conductivity, good chemical stability, and wide electrochemical windows. LATP [Li
1.3 Al0.3 Ti1.7 (PO4 )3 ] solid electrolyte has been widely investigated for its high ionic conductivity. Nevertheless, the chemical instability of LATP against Li metal has hindered its application in solid-state batteries. Here, we propose that atomic layer deposition (ALD) coating on LATP surfaces is able to stabilize the LATP/Li interface by reducing the side reactions. In comparison with bare LATP, the Al2 O3 -coated LATP by ALD exhibits a stable cycling behavior with smaller voltage hysteresis for 600 h, as well as small resistance. More importantly, on the basis of advanced characterizations such as high-resolution transmission electron spectroscope-electron energy loss spectroscopy, the lithium penetration into the LATP bulk and Ti4+ reduction are significantly limited. The results suggest that ALD is very effective in improving solid-state electrolyte/electrode interface stability.- Published
- 2018
- Full Text
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49. Order-level fern plastome phylogenomics: new insights from Hymenophyllales.
- Author
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Kuo LY, Qi X, Ma H, and Li FW
- Subjects
- Biological Evolution, DNA, Plant genetics, Ferns anatomy & histology, Genome, Plant genetics, Genomics, Phylogeny, Polymerase Chain Reaction, Sequence Analysis, DNA, Ferns genetics, Plastids genetics
- Abstract
Premise of the Study: Filmy ferns (Hymenophyllales) are a highly specialized lineage, having mesophyll one-cell layer thick and inhabiting particularly shaded and humid environments. The phylogenetic placement of Hymenophyllales has been inconclusive, and while over 87 whole fern plastomes have been published, none was from Hymenophyllales. To better understand the evolutionary history of filmy ferns, we sequenced the first complete plastome for this order., Methods: We compiled a phylogenomic plastome data set encompassing all 11 fern orders, and reconstructed phylogenies using different data types (nucleotides, codons, and amino acids) and partition schemes (codon positions and loci). To infer the evolution of fern plastome organization, we coded plastome features, including inversions, inverted repeat boundary shifts, gene losses, and tRNA anticodon sequences as characters, and reconstructed the ancestral states for these characters., Key Results: We discovered a suite of novel, Hymenophyllales-specific plastome structures that likely resulted from repeated expansions and contractions of the inverted repeat regions. Our phylogenetic analyses reveal that Hymenophyllales is highly supported as either sister to Gleicheniales or to Gleicheniales + the remaining non-Osmundales leptosporangiates, depending on the data type and partition scheme., Conclusions: Although our analyses could not confidently resolve the phylogenetic position of Hymenophyalles, the results here highlight the danger of drawing conclusions from "all-in" phylogenomic data set without exploring potential inconsistencies in the data. Finally, our first order-level reconstruction of fern plastome structural evolution provides a useful framework for future plastome research., (© 2018 Botanical Society of America.)
- Published
- 2018
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50. Fern genomes elucidate land plant evolution and cyanobacterial symbioses.
- Author
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Li FW, Brouwer P, Carretero-Paulet L, Cheng S, de Vries J, Delaux PM, Eily A, Koppers N, Kuo LY, Li Z, Simenc M, Small I, Wafula E, Angarita S, Barker MS, Bräutigam A, dePamphilis C, Gould S, Hosmani PS, Huang YM, Huettel B, Kato Y, Liu X, Maere S, McDowell R, Mueller LA, Nierop KGJ, Rensing SA, Robison T, Rothfels CJ, Sigel EM, Song Y, Timilsena PR, Van de Peer Y, Wang H, Wilhelmsson PKI, Wolf PG, Xu X, Der JP, Schluepmann H, Wong GK, and Pryer KM
- Subjects
- Ferns microbiology, Gene Duplication genetics, Genes, Plant genetics, Phylogeny, Biological Evolution, Cyanobacteria, Ferns genetics, Genome, Plant genetics, Symbiosis genetics
- Abstract
Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N
2 -fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.- Published
- 2018
- Full Text
- View/download PDF
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