bluuebunny/crossref_metadata_2025_split huggingface dataset:
Searching the web builds fuller picture of arachnid trade
Authors: Marshall Benjamin M. , Strine Colin T. , Fukushima Caroline S. , Cardoso Pedro , Orr Michael C. , Hughes Alice C. 
Published: May 2022

AbstractWildlife trade is a major driver of biodiversity loss, yet whilst the impacts of trade in some species are relatively well-known, some taxa, such as many invertebrates are often overlooked. Here we explore global patterns of trade in the arachnids, and detected 1,264 species from 66 families and 371 genera in trade. Trade in these groups exceeds millions of individuals, with 67% coming directly from the wild, and up to 99% of individuals in some genera. For popular taxa, such as tarantulas up to 50% are in trade, including 25% of species described since 2000. CITES only covers 30 (2%) of the species potentially traded. We mapped the percentage and number of species native to each country in trade. To enable sustainable trade, better data on species distributions and better conservation status assessments are needed. The disparity between trade data sources highlights the need to expand monitoring if impacts on wild populations are to be accurately gauged and the impacts of trade minimised.
The spread of the first introns in proto-eukaryotic paralogs
Authors: Vosseberg Julian , Schinkel Michelle , Gremmen Sjoerd , Snel Berend 
Published: May 2022

AbstractSpliceosomal introns are a unique feature of eukaryotic genes. Previous studies have established that many introns were present in the protein-coding genes of the last eukaryotic common ancestor (LECA). Intron positions shared between genes that duplicated before LECA could in principle provide insight into the emergence of the first introns. In this study we use ancestral intron position reconstructions in two large sets of duplicated families to systematically identify these ancient paralogous intron positions. We found that 20–35% of introns inferred to have been present in LECA were shared between paralogs. These shared introns, which likely preceded ancient duplications, were wide spread across different functions, with the notable exception of nuclear transport. Since we observed a clear signal of pervasive intron loss prior to LECA, it is likely that substantially more introns were shared at the time of duplication than we can detect in LECA. The large extent of shared introns indicates an early origin of introns during eukaryogenesis and suggests an early origin of a nuclear structure, before most of the other complex eukaryotic features were established.
SARS-CoV-2 ORF6 disrupts nucleocytoplasmic trafficking to advance viral replication
Authors: Miyamoto Yoichi , Itoh Yumi , Suzuki Tatsuya , Tanaka Tomohisa , Sakai Yusuke , Koido Masaru , Hata Chiaki , Wang Cai-Xia , Otani Mayumi , Moriishi Kohji , Tachibana Taro , Kamatani Yoichiro , Yoneda Yoshihiro , Okamoto Toru , Oka Masahiro 
Published: May 2022

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF6 is an antagonist of interferon (IFN)-mediated antiviral signaling, achieved through the prevention of STAT1 nuclear localization. However, the exact mechanism through which ORF6 prevents STAT1 nuclear trafficking remains unclear. Herein, we demonstrate that ORF6 directly binds to STAT1 with or without IFN stimulation, resulting in the nuclear exclusion of STAT1. ORF6 also recognizes importin α subtypes with different modes, in particular, high affinity to importin α1 but a low affinity to importin α5. Although ORF6 potentially disrupts the importin α/importin β1-mediated nuclear transport, thereby suppressing the nuclear translocation of the other classical nuclear localization signal-containing cargo proteins, the inhibitory effect of ORF6 is modest when compared with that of STAT1. The results indicate that the drastic nuclear exclusion of STAT1 is attributed to the specific binding with ORF6, which is a distinct strategy for the importin α1-mediated pathway. Combined with the results from a newly-produced replicon system and a hamster model, we conclude that SARS-CoV-2 ORF6 acts as a virulence factor via regulation of nucleocytoplasmic trafficking to accelerate viral replication, resulting in disease progression.
Intrapopulation adaptive variance supports thermal tolerance in a reef-building coral
Authors: Drury Crawford , Bean Nina K. , Harris Casey I. , Hancock Joshua R. , Huckeba Joel , H Christian Martin , Roach Ty N. F. , Quinn Robert A. , Gates Ruth D. 
Published: May 2022

AbstractCoral holobionts are multi-species assemblages, which adds significant complexity to genotype-phenotype connections underlying ecologically important traits like coral bleaching. Small scale heterogeneity in bleaching is ubiquitous in the absence of strong environmental gradients, which provides adaptive variance needed for the long-term persistence of coral reefs. We used RAD-seq, qPCR and LC-MS/MS metabolomics to characterize host genomic variation, symbiont community and biochemical correlates in two bleaching phenotypes of the vertically transmitting coral Montipora capitata. Phenotype was driven by symbiosis state and host genetic variance. We documented 5 gene ontologies that were significantly associated with both the binary bleaching phenotype and symbiont composition, representing functions that confer a phenotype via host-symbiont interactions. We bred these corals and show that symbiont communities were broadly conserved in bulk-crosses, resulting in significantly higher survivorship under temperature stress in juveniles, but not larvae, from tolerant parents. Using a select and re-sequence approach, we document numerous gene ontologies selected by heat stress, some of which (cell signaling, antioxidant activity, pH regulation) have unique selection dynamics in larvae from thermally tolerant parents. These data show that vertically transmitting corals may have an adaptive advantage under climate change if host and symbiont variance interact to influence bleaching phenotype.
IL-33 enhances Jagged1 mediated NOTCH1 intracellular domain (NICD) deubiquitination and pathological angiogenesis in proliferative retinopathy
Authors: Sharma Deepti , Bisen Shivantika , Kaur Geetika , Van Buren Eric C. , Rao Gadiparthi N. , Singh Nikhlesh K. 
Published: May 2022

AbstractPathological retinal neovascularization (NV) is a clinical manifestation of various proliferative retinopathies, and treatment of NV using anti-VEGF therapies is not selective, as it also impairs normal retinal vascular growth and function. Here, we show that genetic deletion or siRNA-mediated downregulation of IL-33 reduces pathological NV in a murine model of oxygen-induced retinopathy (OIR) with no effect on the normal retinal repair. Furthermore, our fluorescent activated cell sorting (FACS) data reveals that the increase in IL-33 expression is in endothelial cells (ECs) of the hypoxic retina and conditional genetic deletion of IL-33 in retinal ECs reduces pathological NV. In vitro studies using human retinal microvascular endothelial cells (HRMVECs) show that IL-33 induces sprouting angiogenesis and requires NFkappaB-mediated Jagged1 expression and Notch1 activation. Our data also suggest that IL-33 enhances de-ubiquitination and stabilization of Notch1 intracellular domain via its interaction with BRCA1-associated protein 1 (BAP1) and Numb in HRMVECs and a murine model of OIR.
Exogenous loading of extracellular vesicles, virus-like particles, and lentiviral vectors with supercharged proteins
Authors: Breyne Koen , Ughetto Stefano , Rufino-Ramos David , Mahjoum Shadi , Grandell Emily A. , de Almeida Luís P. , Breakefield Xandra O. 
Published: May 2022

AbstractCell membrane-based biovesicles (BVs) are important candidate drug delivery vehicles and comprise extracellular vesicles, virus-like particles, and lentiviral vectors. Here, we introduce a non-enzymatic assembly of purified BVs, supercharged proteins, and plasmid DNA called pDNA-scBVs. This multicomponent vehicle results from the interaction of negative sugar moieties on BVs and supercharged proteins that contain positively charged amino acids on their surface to enhance their affinity for pDNA. pDNA-scBVs were demonstrated to mediate floxed reporter activation in culture by delivering a Cre transgene. We introduced pDNA-scBVs containing both a CRE-encoding plasmid and a BV-packaged floxed reporter into the brains of Ai9 mice. Successful delivery of both payloads by pDNA-scBVs was confirmed with reporter signal in the striatal brain region. Overall, we developed a more efficient method to load isolated BVs with cargo that functionally modified recipient cells. Augmenting the natural properties of BVs opens avenues for adoptive extracellular interventions using therapeutic loaded cargo.
Retail prices of nutritious food rose more in countries with higher COVID-19 case counts
Authors: Bai Yan , Costlow Leah , Ebel Alissa , Laves Sarah , Ueda Yurika , Volin Natalie , Zamek Maya , Masters William A. 
Published: May 2022

AbstractThe COVID-19 pandemic has curtailed lives and livelihoods, leading to price spikes for some foods and declines for others. We compare monthly retail food prices in up to 181 countries from January 2019 to June 2021, test for differences over time and find that average prices rose significantly, especially for more nutritious food groups in countries with higher COVID-19 case counts. Analysis of retail prices by food group complements data on farm commodity prices and overall consumer price indexes, helping to guide policy for resilience and response to shocks.
Shoaling of abyssal ventilation in the Eastern Indian Sector of the Southern Ocean
Authors: Shimada Keishi , Kitade Yujiro , Aoki Shigeru , Mizobata Kohei , Cheng Lingqiao , Takahashi Kunio T. , Makabe Ryosuke , Kanda Jota , Odate Tsuneo 
Published: May 2022

AbstractAntarctic Bottom Water formation, which ventilates the abyssal layers of the Southern Ocean, is an integral component of the global ocean meridional overturning circulation. Considering evident freshening and density decreases in the source waters, widespread warming in the Southern Ocean suggests a weakening in the Antarctic Bottom Water supply. We demonstrate that the weakening is robust based on water mass warming in the deep and abyssal layers of the Australian-Antarctic Basin, which remained after removing the southward shift effect of the Southern Antarctic Circumpolar Current Front. Moreover, a decrease in apparent oxygen utilisation and reduced warming in the intermediate density layer below Circumpolar Deep Water extended further from the Australian-Antarctic Basin to the South Australian Basin. We suggest that a concurrent weakening in the densest portion and strengthening in the less dense portion shape the multi-basin change in the meridional overturning circulation that originates from the Southern Ocean.
The role of ocean and atmospheric dynamics in the marine-based collapse of the last Eurasian Ice Sheet
Authors: Sejrup Hans Petter , Hjelstuen Berit Oline , Patton Henry , Esteves Mariana , Winsborrow Monica , Rasmussen Tine Lander , Andreassen Karin , Hubbard Alun 
Published: May 2022

AbstractInformation from former ice sheets may provide important context for understanding the response of today’s ice sheets to forcing mechanisms. Here we present a reconstruction of the last deglaciation of marine sectors of the Eurasian Ice Sheet, emphasising how the retreat of the Norwegian Channel and the Barents Sea ice streams led to separation of the British-Irish and Fennoscandian ice sheets at c. 18.700 and of the Kara-Barents Sea-Svalbard and Fennoscandian ice sheets between 16.000 and 15.000 years ago. Combined with ice sheet modelling and palaeoceanographic data, our reconstruction shows that the deglaciation, from a peak volume of 20 m of sea-level rise equivalent, was mainly driven by temperature forced surface mass balance in the south, and by Nordic Seas oceanic conditions in the north. Our results highlight the nonlinearity in the response of an ice sheet to forcing and the significance of ocean-ice-atmosphere dynamics in assessing the fate of contemporary ice sheets.
Introducing Candidatus Bathyanammoxibiaceae, a family of bacteria with the anammox potential present in both marine and terrestrial environments
Authors: Zhao Rui , Biddle Jennifer F , Jørgensen Steffen L 
Published: May 2022

Abstract
Anaerobic ammonium oxidation (Anammox) bacteria are a group of extraordinary bacteria exerting a major impact on the global nitrogen cycle. Their phylogenetic breadth and diversity, however, are not well constrained. Here we describe a new, deep-branching family in the order of Candidatus Brocadiales, Candidatus Bathyanammoxibiaceae, members of which have genes encoding the key enzymes of the anammox metabolism. In marine sediment cores from the Arctic Mid-Ocean Ridge (AMOR), the presence of Ca. Bathyanammoxibiaceae was confined within the nitrate-ammonium transition zones with the counter gradients of nitrate and ammonium, coinciding with the predicted occurrence of the anammox process. Ca. Bathyanammoxibiaceae genomes encode the core genetic machinery for the anammox metabolism, including hydrazine synthase for converting nitric oxide and ammonium to hydrazine, and hydrazine dehydrogenase for hydrazine oxidation to dinitrogen gas, and hydroxylamine oxidoreductase for nitrite reduction to nitric oxide. Their occurrences assessed by genomes and 16S rRNA gene sequencings surveys indicate that they are present in both marine and terrestrial environments. By introducing the anammox potential of Ca. Bathyanammoxibiaceae and charactering their ideal niche in marine sediments, our findings suggest that the diversity and abundance of anammox bacteria may be higher than previously thought, and provide important insights on cultivating them in the future to not only assess their biogeochemical impacts but also constrain the emergence and evolutionary history of this functional guild on Earth.
Estimating the COVID-19 infection fatality ratio accounting for seroreversion using statistical modelling
Authors: Brazeau Nicholas F. , Verity Robert , Jenks Sara , Fu Han , Whittaker Charles , Winskill Peter , Dorigatti Ilaria , Walker Patrick G. T. , Riley Steven , Schnekenberg Ricardo P. , Hoeltgebaum Henrique , Mellan Thomas A. , Mishra Swapnil , Unwin H. Juliette T. , Watson Oliver J. , Cucunubá Zulma M. , Baguelin Marc , Whittles Lilith , Bhatt Samir , Ghani Azra C. , Ferguson Neil M. , Okell Lucy C. 
Published: May 2022

AbstractBackgroundThe infection fatality ratio (IFR) is a key statistic for estimating the burden of coronavirus disease 2019 (COVID-19) and has been continuously debated throughout the COVID-19 pandemic. The age-specific IFR can be quantified using antibody surveys to estimate total infections, but requires consideration of delay-distributions from time from infection to seroconversion, time to death, and time to seroreversion (i.e. antibody waning) alongside serologic test sensitivity and specificity. Previous IFR estimates have not fully propagated uncertainty or accounted for these potential biases, particularly seroreversion.MethodsWe built a Bayesian statistical model that incorporates these factors and applied this model to simulated data and 10 serologic studies from different countries.ResultsWe demonstrate that seroreversion becomes a crucial factor as time accrues but is less important during first-wave, short-term dynamics. We additionally show that disaggregating surveys by regions with higher versus lower disease burden can inform serologic test specificity estimates. The overall IFR in each setting was estimated at 0.49–2.53%.ConclusionWe developed a robust statistical framework to account for full uncertainties in the parameters determining IFR. We provide code for others to apply these methods to further datasets and future epidemics.
Trajectory patterns of SARS-CoV-2 neutralising antibody response in convalescent COVID-19 patients
Authors: Wong Ngai Sze , Lee Shui Shan , Chan Denise P. C. , Li Timothy C. M. , Ho Tracy H. Y. , Luk Fion W. L. , Chow Kai Ming , Tso Eugene Y. K. , Yeoh Eng-Kiong , Wong Samuel Y. S. , Hui David S. C. , Lui Grace C. Y. 
Published: May 2022

Abstract
Background
The adaptive immune responses of COVID-19 patients contributes to virus clearance, restoration of health and protection from re-infection. The patterns of and the associated characteristics with longitudinal neutralising antibody (NAb) response following SARS-CoV-2 infection are important in their potential association with the population risks of re-infection.

Methods
This is a longitudinal study with blood samples and clinical data collected in adults aged 18 or above following diagnosis of SARS-CoV-2 infection. NAb levels were measured by the SARS-CoV-2 surrogate virus neutralisation test (sVNT). Anonymous clinical and laboratory data were matched with surveillance data for each subject for enabling analyses and applying latent class mixed models for trajectory delineation. Logistic regression models were performed to compare the characteristics between the identified classes.

Results
In 2020–2021, 368 convalescent patients in Hong Kong are tested for NAb. Their seroconversion occur within 3 months in 97% symptomatic patients, the level of which are maintained at 97% after 9 months. The NAb trajectories of 200 symptomatic patients are classified by the initial response and subsequent trend into high-persistent and waning classes in latent class mixed models. High-persistent (15.5%) class patients are older and most have chronic illnesses. Waning class patients (84.5%) are largely young adults who are mildly symptomatic including 2 who serorevert after 10 months.

Conclusions
Characteristic sub-class variabilities in clinical pattern are noted especially among patients with waning NAb. The heterogeneity of the NAb trajectory patterns and their clinical association can be important for informing vaccination strategy to prevent re-infection.
Synthesis of a Möbius carbon nanobelt
Authors: Segawa Yasutomo , Watanabe Tsugunori , Yamanoue Kotono , Kuwayama Motonobu , Watanabe Kosuke , Pirillo Jenny , Hijikata Yuh , Itami Kenichiro 
Published: May 2022

AbstractTechnologies for the creation of topological carbon nanostructures have greatly advanced synthetic organic chemistry and materials science. Although simple molecular nanocarbons with a belt topology have been constructed, analogous carbon nanobelts with a twist—more specifically, Möbius carbon nanobelts (MCNBs)—have not yet been synthesized owing to their high intrinsic strain. Here we report the synthesis, isolation and characterization of a MCNB. Calculations of strain energies suggest that large MCNBs are synthetically accessible. Designing a macrocyclic precursor with an odd number of repeat units led to a successful synthetic route via Z-selective Wittig reactions and nickel-mediated intramolecular homocoupling reactions, which yielded (25,25)MCNB over 14 steps. NMR spectroscopy and theoretical calculations reveal that the twist moiety of the Möbius band moves quickly around the MCNB molecule in solution. The topological chirality that originates from the Möbius structure was confirmed experimentally using chiral HPLC separation and circular dichroism spectroscopy.
Performance analysis of RIS aided NOMA networks with hardware impairments
Authors: Lu Zhiping , Yue Xinwei , Chen Shuo , Ma Weiguo 
Published: May 2022

AbstractReconfigurable intelligent surface (RIS) has stimulated their potential applications for improving the performance of wireless communication networks. In this paper, the performance of RIS aided non‐orthogonal multiple access (NOMA) networks with hardware impairments over Rician fading channels is investigated. More specifically, the exact and asymptotic expressions of outage probability for a pair of users, that is, the nearby user n and distant user m are derived, where the imperfect successive interference cancellation (ipSIC) and perfect SIC (pSIC) are taken into consideration. According to the approximate analyses, the diversity orders of user n with ipSIC/pSIC and user m are obtained in the high signal‐to‐noise radio regime. It indicates that the diversity orders are in connection with reflecting elements and Rician factors except the channel ordering. The impact of these parameters on outage behaviors of RIS‐NOMA networks is also analysed. In addition, the system throughput of RIS‐NOMA networks with ipSIC/pSIC is surveyed in detail. Monte Carlo simulations are present to verify the correctness of theoretical analyses that: (1) The outage probability of user n with pSIC is superior to that of orthogonal user, while the outage probability of user m is inferior to that of orthogonal user and (2) as the number of reflecting elements and Rician factors increases, the outage behaviors of RIS‐NOMA networks are enhanced carefully.
Direction of arrival estimation under Class A modelled noise in shallow water using variational Bayesian inference method
Authors: Feng Xiao , Zhang Xuebo , Song Ruiping , Wang Junfeng , Sun Haixin , Esmaiel Hamada 
Published: May 2022

AbstractThe shallow water noise shows obvious impulsive property, which greatly degrades the direction of arrival (DOA) performance due to the conventional design concept based on the Gaussian assumption. In this paper, DOA estimator in presence of impulsive noise utilising variational Bayesian inference is proposed. The Middleton's Class A noise model is considered as a typical underwater noise model to analyse the performance of DOA estimation. The DOA estimation problem is modelled as the sparse signal recovery problem, and the hierarchical Bayesian learning framework is formulated by considering the common sparsity of signal and the element‐wise sparsity of the impulsive noise. The variational Bayesian inference realises the posterior estimation of signal and impulsive noise components. To mitigate the basis mismatches, the root sparse Bayesian learning method is applied to refine the steering vectors. Simulations verify the advantages of the proposed DOA method in terms of spatial resolution, root mean square error, accuracy, and robustness compared with the state‐of‐the‐art benchmarks in the presence of Middleton's Class A noise.