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Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam
PeerJ - Tập 12 - Trang e17553 - 2024
Nam-Hai Truong, Thi-Thu-Hong Le, Hong-Duong Nguyen, Hong-Thanh Nguyen, Trong-Khoa Dao, Thi-Minh-Nguyet Tran, Huyen-Linh Tran, Dinh-Trong Nguyen, Thi-Quy Nguyen, Thi-Hong-Thao Phan, Thi-Huyen Do, Ngoc-Han Phan, Thi-Cam-Nhung Ngo, Van-Van Vu
#Chitin-active and cellulose-active LPMOs; Metagenomics; Fungal-bacterialrelationships; Protein spatial conformation prediction
A new paravian dinosaur from the Late Jurassic of North America supports a late acquisition of avian flight
PeerJ - Tập 7 - Trang e7247
Scott Hartman, Mickey Mortimer, William R. Wahl, Dean R. Lomax, Jessica Lippincott, David M. Lovelace
The last two decades have seen a remarkable increase in the known diversity of basal avialans and their paravian relatives. The lack of resolution in the relationships of these groups combined with attributing the behavior of specialized taxa to the base of Paraves has clouded interpretations of the origin of avialan flight. Here, we describeHesperornithoides miesslerigen. et sp. nov., a new paravian theropod from the Morrison Formation (Late Jurassic) of Wyoming, USA, represented by a single adult or subadult specimen comprising a partial, well-preserved skull and postcranial skeleton. Limb proportions firmly establishHesperornithoidesas occupying a terrestrial, non-volant lifestyle. Our phylogenetic analysis emphasizes extensive taxonomic sampling and robust character construction, recovering the new taxon most parsimoniously as a troodontid close toDaliansaurus,Xixiasaurus, andSinusonasus. Multiple alternative paravian topologies have similar degrees of support, but proposals of basal paravian archaeopterygids, avialan microraptorians, andRahonavisbeing closer to Pygostylia than archaeopterygids or unenlagiines are strongly rejected. All parsimonious results support the hypothesis that each early paravian clade was plesiomorphically flightless, raising the possibility that avian flight originated as late as the Late Jurassic or Early Cretaceous.
Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity
PeerJ - Tập 2 - Trang e573
Hannah L. Buckley, Arash Rafat, Johnathon Ridden, Robert Cruickshank, Hayley J. Ridgway, Adrian M. Paterson
Osteology and phylogeny ofRobustichthys luopingensis, the largest holostean fish in the Middle Triassic
PeerJ - Tập 7 - Trang e7184
Guanghui Xu
The extinct ray-finned fish taxonRobustichthys luopingensisfrom Luoping, eastern Yunnan, China represents the largest holostean known in the Middle Triassic. Despite its potential significance for investigating the holostean phylogeny and reconstructing the Triassic marine ecosystems,Robustichthyshas so far not been described in detail and its phylogenetic position within the Holostei was controversy. This study provides a redescription and revision ofRobustichthysbased upon a comparative study of eight type specimens and nine new specimens. Newly recognized information includes a toothed parasphenoid, a pair of premaxillae not pierced by the olfactory nerve, a splint-like quadratojugal, a hatchet-shaped hyomandibula, an hourglass-shaped symplectic, anterior and posterior ceratohyals, a complete series of branchiostegal rays, and sclerotic bones. A revised reconstruction ofRobustichthysis presented. Results of a cladistic analysis confirmedRobustichthysas an ionoscopiform within the Halecomorphi; the previous placements ofRobustichthysas a basal ginglymodian and Ionoscopidae as a basal amiiform clade are not supported. The sister group relationship between Sinamiinae (SinamiaandIkechaoamia) and Amiinae (AmiaandCyclurus) within the Amiidae is newly recognized. This revised topology provides new insights into the evolution and historical paleoecology of halecomorph fishes.
Is there a link between pre-existing antibodies acquired due to childhood vaccinations or past infections and COVID-19? A case control study
PeerJ - Tập 9 - Trang e10910
Bilge Sümbül, Hilmi Erdem Sümbül, Ramazan Azim Okyay, Erdinç Gülümsek, Ahmet Rıza Şahin, Barış Boral, Burhan Fatih Koçyiğit, Mostafa Alfishawy, Jeffrey Gold, Ali Muhittin Taşdoğan
Background There is growing evidence indicating that children are less affected from COVID-19. Some authors speculate that childhood vaccinations may provide some cross-protection against COVID-19. In this study, our aim was to compare the circulating antibody titers for multiple childhood vaccine antigens, as an indicator of the state of immune memory between patients with COVID-19 and healthy controls, with a specific aim to identify the association between disease severity and antibody titrations which may indicate a protective function related to vaccine or disease induced memory. Methods This study is a case-control study including 53 patients with COVID-19 and 40 healthy volunteers. COVID-19 severity was divided into three groups: asymptomatic, mild and severe. We measured the same set of antibody titers for vaccine antigens, and a set of biochemical and infection markers, in both the case and control groups. Results Rubella (p = 0.003), pneumococcus (p = 0.002), and Bordetella pertussis (p < 0.0001) titers were found to be significantly lower in the case group than the control group. There was a significant decline in pneumococcus titers with severity of disease (p = 0.021) and a significant association with disease severity for Bordetella pertussis titers (p = 0.014) among COVID patients. Levels of AST, procalcitonin, ferritin and D-dimer significantly increased with the disease severity. Discussion Our study supports the hypothesis that pre-existing immune memory, as monitored using circulating antibodies, acquired from childhood vaccinations, or past infections confer some protection against COVID-19. Randomized controlled studies are needed to support a definitive conclusion.
Identification of priority shorebird conservation areas in the Caribbean
PeerJ - Tập 8 - Trang e9831
Jessica Rozek Cañizares, J. Michael Reed
Despite being geographically central to the Atlantic Americas Flyway for migratory birds, the Caribbean is often overlooked or underappreciated when addressing the conservation of North American shorebirds. To our knowledge, this is the first Caribbean-wide assessment of shorebird use in the region. We analyzed 211,013 shorebird species observations in the insular Caribbean from 2010–2019, representing 78,794 eBird checklists and cumulative total of 2.1 million shorebirds of 45 species. We conclude that priority areas for shorebird conservation include Humedal Sur de Pinar del Río (Humedal Sur de Los Palacios) in Cuba, and Monte Cristi in the Dominican Republic as they each likely support more than 20,000 shorebirds annually, and they host large abundances of geographic populations for particular taxa. Specifically, the former site hosts >10% of Short-billed Dowitchers (Limnodromus griseus griseus/hendersoni), and >1% of Black-bellied Plovers (Pluvialis squatarola cynosurae) and Wilson’s Plovers (Charadrius wilsonia wilsonia), while the latter site supports large numbers of Black-necked Stilts (Himantopus mexicanus).We also identified at least 15 additional sites that likely cross the 1% population threshold for one or more shorebird taxa. These sites may qualify for special international designations such as Important Bird and Biodiversity Areas or as part of the Western Hemisphere Shorebird Reserve Network; 11 of the 17 sites we identified do not hold either of these titles. Data on subspecific or geographic distributions of three species, Snowy Plover (C. nivosus), Black-necked Stilt, and Killdeer (C. vociferous), are insufficient to reveal if the sites with the highest abundances were mostly comprised of Caribbean populations or migrants, but the limited information suggests that they also likely exceed 1% thresholds on several islands. Based on our results, we recommend more extensive systematic surveys of shorebirds in the Caribbean, including research on turnover rates and movements between islands, as well as assimilation of shorebird survey data not yet included in the eBird portal.
Survey of owner motivations and veterinary input of owners feeding diets containing raw animal products
PeerJ - Tập 5 - Trang e3031
Stewart K. Morgan, Susan Willis, Megan Shepherd
BackgroundThe practice of feeding of diets containing raw animal products (RAP) to pets (dogs and cats) is discouraged by veterinary organizations and governmental public health organizations. Nevertheless, the practice of feeding RAP to pets is increasing in popularity. Pet owner motivations for feeding RAP diets to pets have not been explored and the benefits of RAP diets remain largely anecdotal. We hypothesized that pet owners feeding RAP diets would not rely on veterinary advice in choosing their pet’s diet. We also hypothesized that these owners would have lower levels of trust in veterinary advice with respect to nutrition relative to pet owners not feeding RAP.MethodsAn anonymous web-based survey was developed to identify pet owner motivations for feeding RAP diets, and to characterize the veterinarian-client relationships of individuals feeding RAP diets.ResultsThere were 2,337 respondents and 2,171 completed surveys. Of survey respondents, 804 reported feeding RAP at the time of the survey. While 20% of pet owners feeding RAP relied on online resources to determine what or how much RAP to feed, only 9% reported consulting with a veterinarian in making decisions about feeding RAP. Pet owners feeding RAP reported lower levels of trust in veterinary advice both ‘in general’ and ‘with respect to nutrition’ than pet owners not feeding RAP. Most pet owners reported that a discussion regarding their pet’s nutrition does not occur at every veterinary appointment.DiscussionPet owners feeding a RAP diet have lower trust in veterinary advice than pet owners not feeding a RAP diet. Owners feeding RAP are more reliant on online resources than their own veterinarian in deciding what and how much RAP to feed. Pet owners perceive that nutrition is not discussed at most veterinary appointments. Therefore, there is room for improvement in the veterinarian-client communication with regards to nutrition.
So sánh dược động học của quercetin, isoquercitrin và quercetin-3-O-β-D-glucuronide ở chuột bằng HPLC-MS Dịch bởi AI
PeerJ - Tập 7 - Trang e6665
Hongli Yin, Ji Ma, Jichun Han, Maoru Li, Jing Shang
Giới thiệu Quercetin (Qr), isoquercitrin (IQ) và quercetin-3-O-β-D-glucuronide (QG) là những chất thực vật mạnh có khả năng phòng chống bệnh và cải thiện sức khỏe. Tuy nhiên, có thể tồn tại sự chuyển hoá giữa Qr, IQ và QG trong cơ thể. Cần có sự nghiên cứu hệ thống về dược động học của Qr, IQ và QG để hiểu rõ hơn về hành động dược lý của chúng. Phương pháp Chúng tôi đã phát triển một phương pháp HPLC-MS đáng tin cậy để so sánh dược động học của Qr, IQ và QG sau khi cho chuột uống riêng từng chất (50 mg/kg), sử dụng puerarin làm tiêu chuẩn nội bộ. Phát hiện được thực hiện bằng cách giám sát ion chọn lọc âm tính. Phương pháp này được xác nhận về độ chọn lọc, độ tuyến tính, độ chính xác, độ tái lập, khả năng thu hồi trích xuất, hiệu ứng ma trận và độ ổn định; và cho thấy độ tin cậy trong việc giám sát sự hành động dược động học của ba hợp chất này. Kết quả Kết quả của chúng tôi cho thấy sau khi uống riêng quercetin, IQ và QG, tất cả các hợp chất đều có thể được phát hiện trong huyết tương. Ngoài ra, QG có thể được phát hiện trong nhóm Qr; Qr và QG có thể được đo trong nhóm IQ; và Qr có thể được tìm thấy trong huyết tương chuột sau 1.5 giờ kể từ khi dùng QG. Hơn thế nữa, AUC0−t của Qr trong nhóm Qr (2,590.5 ± 987.9 mg/L*phút), nhóm IQ (2,212.7 ± 914.1 mg/L*phút), và nhóm QG (3,505.7 ± 1,565.0 mg/L*phút) lớn hơn AUC0−t của QG trong nhóm Qr (1,550.0 ± 454.2 mg/L*phút), nhóm IQ (669.3 ± 188.3 mg/L*phút), và nhóm QG (962.7 ± 602.3 mg/L*phút). AUC0−t của IQ là thấp nhất trong tất cả các nhóm. Thảo luận Quercetin, IQ và QG đều có thể hấp thụ vào huyết tương. Tồn tại sự chuyển hóa qua lại giữa Qr và QG, và IQ có thể được chuyển hóa thành Qr và QG trong chuột SD. Những kết quả này cung cấp cơ sở có ý nghĩa để hiểu rõ hành động dược lý của ba hợp chất này.
#quercetin #isoquercitrin #quercetin-3-O-β-D-glucuronide #HPLC-MS #dược động học #chuột #hấp thụ #chuyển hóa #tác động dược lý
Forecasting influenza epidemics by integrating internet search queries and traditional surveillance data with the support vector machine regression model in Liaoning, from 2011 to 2015
PeerJ - Tập 6 - Trang e5134
Feng Liang, Peng Guan, Wei Wu, Desheng Huang
Background Influenza epidemics pose significant social and economic challenges in China. Internet search query data have been identified as a valuable source for the detection of emerging influenza epidemics. However, the selection of the search queries and the adoption of prediction methods are crucial challenges when it comes to improving predictions. The purpose of this study was to explore the application of the Support Vector Machine (SVM) regression model in merging search engine query data and traditional influenza data. Methods The official monthly reported number of influenza cases in Liaoning province in China was acquired from the China National Scientific Data Center for Public Health from January 2011 to December 2015. Based on Baidu Index, a publicly available search engine database, search queries potentially related to influenza over the corresponding period were identified. An SVM regression model was built to be used for predictions, and the choice of three parameters (C, γ, ε) in the SVM regression model was determined by leave-one-out cross-validation (LOOCV) during the model construction process. The model’s performance was evaluated by the evaluation metrics including Root Mean Square Error, Root Mean Square Percentage Error and Mean Absolute Percentage Error. Results In total, 17 search queries related to influenza were generated through the initial query selection approach and were adopted to construct the SVM regression model, including nine queries in the same month, three queries at a lag of one month, one query at a lag of two months and four queries at a lag of three months. The SVM model performed well when with the parameters (C = 2, γ = 0.005, ɛ = 0.0001), based on the ensemble data integrating the influenza surveillance data and Baidu search query data. Conclusions The results demonstrated the feasibility of using internet search engine query data as the complementary data source for influenza surveillance and the efficiency of SVM regression model in tracking the influenza epidemics in Liaoning.
Impact of polystyrene microplastics on Daphnia magna mortality and reproduction in relation to food availability
PeerJ - Tập 6 - Trang e4601
Rana Al-Jaibachi, Amanda Callaghan
Microplastics (MPs) in the environment continue to be a growing area of concern in terms of acute and chronic impacts on aquatic life. Whilst increasing numbers of studies are providing important insights into microparticle behaviour and impacts in the marine environment, a paucity of information exists regarding the freshwater environment. This study focusses on the uptake, retention and the impact of 2 µm polystyrene MPs in the freshwater cladoceran Daphnia magna in relation to food intake (algae Chlorella vulgaris), with MP size chosen to approximately match the cell size of the algae. Daphnia were exposed to varied concentrations of MPs and algae. When exposed to a single concentration of MPs Daphnia almost immediately ate them in large quantities. However, the presence of algae, even at low concentrations, had a significant negative impact on MP uptake that was not in proportion to relative availability. As MP concentrations increased, intake did not if algae were present, even at higher concentrations of MPs. This suggests that Daphnia are selectively avoiding eating plastics. Adult Daphnia exposed to MPs for 21 days showed mortality after seven days of exposure in all treatments compared to the control. However significant differences were all related to algal concentration rather than to MP concentration. This suggests that where ample food is present, MPs have little effect on adults. There was also no impact on their reproduction. The neonate toxicity test confirmed previous results that mortality and reproduction was linked to availability of food rather than MP concentrations. This would make sense in light of our suggestion that Daphnia are selectively avoiding eating microplastics.
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