bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new classification of Cyperaceae (Poales) supported by phylogenomic data
Authors: Larridon Isabel , Zuntini Alexandre R. , Léveillé‐Bourret Étienne , Barrett Russell L. , Starr Julian R. , Muasya A. Muthama , Villaverde Tamara , Bauters Kenneth , Brewer Grace E. , Bruhl Jeremy J. , Costa Suzana M. , Elliott Tammy L. , Epitawalage Niroshini , Escudero Marcial , Fairlie Isabel , Goetghebeur Paul , Hipp Andrew L. , Jiménez‐Mejías Pedro , Sabino Kikuchi Izai A.B. , Luceño Modesto , Márquez‐Corro José Ignacio , Martín‐Bravo Santiago , Maurin Olivier , Pokorny Lisa , Roalson Eric H. , Semmouri Ilias , Simpson David A. , Spalink Daniel , Thomas W. Wayt , Wilson Karen L. , Xanthos Martin , Forest Félix , Baker William J. 
Published: May 2021

AbstractCyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology due to their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including multiple origins of C4 photosynthesis and holocentric chromosomes. Goetghebeur′s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower, and embryo characters, plus anatomical and other information. Since then, several family‐level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after the last comprehensive classification of the family, we present the first family‐wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. In addition, 62 accessions available from GenBank were mined for overlapping reads and included in the phylogenomic analyses. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal, and generic levels is proposed. The majority of previously recognized suprageneric groups are supported, and for the first time, we establish support for tribe Cryptangieae as a clade including the genus Koyamaea. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes, and 10 subtribes, and basic information on the 95 genera. The classification includes five new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, and Oreobolinae.
Risk of transmittable blood‐borne pathogens in blood units from blood donor dogs in Canada
Authors: Nury Charlotte , Blais Marie‐Claude , Arsenault Julie 
Published: May 2021

AbstractBackgroundCanine blood donors can be infected by various vector‐borne or other pathogens that could be an important cause of morbidity and death in transfusion recipients.Hypothesis/ObjectivesTo estimate and predict positivity to transmittable blood‐borne pathogens in blood units collected from blood donor dogs in Canada.AnimalsSix thousand one hundred and fifty blood units from 1914 active blood donors registered to the Canadian Animal Blood Bank (CABB) between March 2010 and December 2016.MethodsA registry‐based retrospective study. Blood units were screened by SNAP 4Dx/4Dx Plus and PCR panel tests. Information on blood donors and test results were extracted from multiple databases and collated. Logistic regressions were used to predict blood unit positivity.ResultsOf 1779 blood units, 0.56% were antibody‐positive forAnaplasma phagocytophilum/platysand 0% forEhrlichia canis/ewingii. After exclusion of antibody‐positive units toAnaplasmaspp., 1.1% of 6140 blood units were PCR‐positive toAnaplasma phagocytophilum,Bartonellaspp.,Brucella canis, “CandidatusMycoplasma haematoparvum,”Mycoplasma haemocanis, or a combination of these pathogens.Babesiaspp.,Ehrlichiaspp., andLeishmaniaspp. were not detected. Units from the first blood collection from a dog had higher odds of testing PCR‐positive (P< .001) for at least 1 pathogen than units from subsequent collections.Conclusions and Clinical ImportanceAlthough our study indicates a low probability of detecting blood‐borne pathogen in blood units collected by this Canadian blood bank, the presence of positive units highlights the importance of the preemptive identification and screening of blood units from healthy blood donors for safe blood banking, especially in first‐time donors.
Comparison of oral, nebulized and combination antibiotic treatment ofBordetellabronchisepticain baboons (Papiospp.)
Authors: Clemmons Elizabeth A. , Chavez Deborah , Condel Laura , Dutton John W. , Price Sharon , Lanford Robert 
Published: May 2021

AbstractIncidence ofBordetella pertussis, the causative agent of whooping cough, is rising in some global human populations despite high vaccination rates, and significant research is underway to address the issue. Baboons are an established model for pertussis research, but like many mammals, they can be naturally infected withBordetella bronchiseptica. BecauseB. bronchisepticainterferes withB. pertussisresearch, it must be excluded from baboons under consideration for enrollment in pertussis studies. In addition to research‐related concerns,B. bronchisepticacan sometimes cause clinical disease in baboons and other nonhuman primates. This study examined the use of antibiotics to clearB. bronchisepticain naturally infected baboons. Thirty‐five juvenile baboons were divided into five treatment groups: oral sulfamethoxazole/trimethoprim (TMS), nebulized gentamicin (gentamicin), combination (TMS + gentamicin) in positive animals, combination (TMS + gentamicin) as a prophylactic in exposed animals and no treatment (control). Combination of oral TMS and nebulized gentamicin given to positive animals was most effective, producing long‐term clearance in 11 out of 12 treated animals. To avoid unnecessary use of antibiotics, our primary management strategy is screening and separating to allow natural clearance and limiting exposure to non‐infected animals, but this study investigates an antibiotic regimen that could be used in special circumstances.
Opportunities for U.S. marine finfish aquaculture
Authors: Rexroad Caird , Rust Michael B. , Riche Martin , Wills Paul , Davis Megan 
Published: May 2021

AbstractExpanding aquaculture production in the United States affords opportunities to complement fisheries in meeting domestic demand for seafood. This access to safe, affordable, and healthy food choices is provided with minimal impacts on the environment and in concert with the many uses required of our water resources. The United States has a strong history of well‐managed fisheries; however, with harvests near their maximum sustainable capacity, meeting current and future demands for seafood may best be accomplished through development of aquaculture. In fact, this is already happening, but mostly outside of the United States. Over 85% of the seafood Americans eat is imported, half is produced through foreign aquaculture; therefore, expanding aquaculture in the United States is a logical approach for reducing our $16.8 billion seafood trade deficit along with other benefits of local production. This series of articles on the development of marine finfish species for commercial aquaculture production is a part of the effort to spur domestic growth in marine finfish aquaculture. The articles in this volume provide up‐to‐date scientific and technical knowledge needed to sustainably produce safe and nutritious fish that will lead to the creation of new economic opportunities through aquaculture in rural, urban, coastal, and inland communities.
Factors affecting the spatial distribution and co‐occurrence of two sympatric mountain ungulates in southern Mongolia
Authors: Odonjavkhlan C. , Alexsander J.S. , Mishra C. , Samelius G. , Sharma K. , Lkhagvajav P. , Suryawanshi K.R. 
Published: May 2021

AbstractCo‐occurrence of ungulates in multi‐species assemblages has fascinated ecologists because these species seemingly belong to the same guild – feeding on plants. Across large parts of the high mountains of Central Asia, ibex (Capra sibirica) and argali (Ovis ammon), both predominantly grazers, co‐occur at local and regional scales. However, little is known about the ecological and anthropogenic factors that influence their spatial distribution, co‐occurrence and habitat use. We examined factors affecting the distribution and co‐occurrence of these two sympatric species in Tost Tosonbumba Nature Reserve in southern Mongolia using an occupancy modeling approach. Specifically, we used single species occupancy models to examine the influence of road density, livestock density, terrain ruggedness and elevation on occupancy of these two species separately. We then assessed how these two species influence each other's distribution by using multi‐species occupancy models. The model‐averaged occupancy probabilities for ibex and argali were 0.64 ± 0.3 se and 0.44 ± 0.2 se, respectively. Terrain ruggedness positively influenced ibex distribution, while it negatively affected the occupancy of argali. We found limited evidence of relationship with factors associated with human disturbance. The species interaction factor, which indicates the level of co‐occurrence, suggested that ibex and argali occurred independent of each other ( = 0.72 ± 0.3 se). Together, our results imply that there was limited co‐occurrence between the two species and that this was largely driven by terrain ruggedness at the scale of the home range. These results suggest that topography plays an important role in enabling these two species to co‐occur at the regional scale.
Reproductive success, apparent survival, and ventral blue coloration in male prairie lizards (Sceloporus consobrinus)
Authors: Robinson C. D. , Lance S. L. , Gifford M. E. 
Published: May 2021

AbstractColoration can evolve in response to selection targeting colorful traits that affect survival or reproductive success. Trait covariation can complicate evolutionary dynamics when selection on covarying traits acts antagonistically. In prairie lizards (Sceloporus consobrinus), males exhibit blue ventral patches that are reduced in females. The development of ventral coloration corresponds with increases of circulating testosterone at sexual maturity. Previous work has illustrated that testosterone and coloration covary, such that individuals with higher testosterone have bluer patches. However, testosterone is known to increase mortality in many organisms, including Sceloporus, so selection against high testosterone can lead to indirect selection against bluer males. While previous work has suggested that patch coloration does not affect fitness, this has not yet been explicitly tested using estimates of survival and reproductive success. Here, we quantify patch coloration, apparent survival, encounter probability, and reproductive success in a wild population of male prairie lizards to assess the role of patch color variation on fitness. Specifically, we tested how patch coloration affects survival and reproductive success across 2 years. We found that none of the patch phenotypes we measured covaried with fitness, suggesting that neither natural nor sexual selection act, or act very weakly, on patch morphology. We found evidence of sexual selection on body size, such that larger males sired more offspring, likely through increased activity. However, this result was inconsistent, as it was only found in one year. Interestingly, we found that, in both years, bluer males were more likely to sire at least one offspring, suggesting some role of patch coloration in reproduction, although we cannot detect what that role may be. Overall, our study suggests that neither apparent survival nor reproductive success is strong drivers of the evolution of ventral coloration in S. consobrinus.
Kinetics of the neutrophil‐lymphocyte ratio during PD‐1 inhibition as a prognostic factor in advanced hepatocellular carcinoma
Authors: Choi Won‐Mook , Kim Ji Yoon , Choi Jonggi , Lee Danbi , Shim Ju Hyun , Lim Young‐Suk , Lee Han Chu , Yoo Changhoon , Ryu Min‐Hee , Ryoo Baek‐Yeol , Kim Kang Mo 
Published: May 2021

AbstractBackground and AimsProgrammed death 1 (PD‐1) inhibitors have improved survival outcomes and produced durable responses in advanced hepatocellular carcinoma (HCC) for some patients. Here, we evaluated the relationship between the baseline and kinetics of the neutrophil‐lymphocyte ratio (NLR) and clinical outcomes in nivolumab‐treated HCC patients.MethodsAll consecutive HCC patients treated with nivolumab between July 2017 and June 2020 were screened for the eligibility. The NLRs were calculated before and at 2, 4 and 6 weeks after treatment. Survival outcomes were compared based on the baseline and kinetics of NLR. We additionally analysed the association of the baseline and dynamic changes in the NLR with hyperprogression (HPD).ResultsAmong the 194 included cases, most patients were male (82.0%) and had a Child–Pugh Class A disease (70.6%). Patients with a baseline NLR ≥ 3 (hazard ratio [HR] 2.46; 95% CI 1.63‐3.71) had a poorer overall survival than patients with baseline NLR < 3. During the treatment, the NLR increased rapidly in patients developing HPD, and only a ΔNLR at 4 weeks was predictive of HPD. The risk of HPD increased by 20% for every 20% increase in the ΔNLR at 4 weeks. Accordingly, an NLR increase at 4 weeks (HR 1.79; 95% CI 1.19‐2.68) was associated with an increased risk of death, especially among patients with a baseline NLR ≥ 3.ConclusionsThe baseline and on‐treatment kinetics for the NLR are effective prognostic indicators in nivolumab‐treated patients with HCC. This may help to guide patient selection and on‐treatment strategies for immunotherapies in advanced HCC.
Serum testosterone levels and testosterone supplementation in cirrhosis: A systematic review
Authors: Deng Nanfu , Mallepally Niharika , Peng Frederick B. , Kanji Aleem , Marcelli Marco , Hernaez Ruben 
Published: May 2021

AbstractBackground & AimsCirrhosis disrupts the hypothalamic–pituitary–gonadal axis causing low testosterone. Testosterone deficiency is associated with sarcopenia and osteopenia, leading to a state of frailty and worse clinical outcomes, morbidity and mortality. We aimed to conduct a systematic review on the relationship between serum testosterone and laboratory, anthropometric and clinical outcomes in observational and interventional studies in cirrhosis.MethodsPubMed and EMBASE were searched from inception through 27 August 2020 and reviewed independently by two investigators; a third reviewer solved disagreement. A qualitative summary of relevant findings was done. Methodological quality was assessed using the Newcastle Ottawa Scale for non‐interventional studies and the Cochrane Risk of Bias for interventional studies.ResultsOut of 3569 articles, 15 met inclusion criteria with six observational studies of 1267 patients and nine interventional studies of 580 patients. In observational studies, low serum testosterone level was associated with sarcopenia, shorter median time to hepatic decompensation, transplant requirement, higher model for end‐stage liver disease (MELD) scores, and death in cirrhotic patients. Nine interventional studies (361 treated with testosterone vs 219 placebo, 1‐36 months) showed that testosterone supplementation improved serum testosterone, appendicular mass and bone mineral density. However, no trial reported improvement in liver‐related scores, complications, readmission rates or death.ConclusionsLow serum testosterone is associated with increased morbidity and mortality in cirrhosis patients. Testosterone supplementation improved intermediate endpoints, but there was no conclusive data on clinical outcomes. Testosterone supplementation may be a promising strategy to improve frailty and decrease significant clinical complications in cirrhosis.
Immunogenicity and safety of HBAI20 Hepatitis B vaccine in non‐responders: Double‐blinded, randomised, controlled phase 2 trial
Authors: Koc Özgür M. , de Smedt Philippe , Kremer Cécile , Robaeys Geert , van Damme Pierre , Hens Niel , Almeida Jorge , Falkenberg Frank , Savelkoul Paul , Oude Lashof Astrid ,   the BE RESPONDER Study Group
Published: May 2021

AbstractBackground & AimsApproximately 5%–10% of the general population respond inadequately to licensed recombinant hepatitis B vaccines. We assessed the immunogenicity and safety of a new HBAI20 vaccine, consisting of a new AI20 adjuvant (20‐µg recombinant human IL‐2 attached to 20‐µg aluminium hydroxide) in combination with HBVaxPro®‐10 µg.MethodsIn a double‐blinded, randomised, controlled phase 2 trial, 18‐ to 59‐year‐old healthy non‐responders (titre <10 mIU/ml after three or more doses of hepatitis B vaccine) were assigned (3:1 ratio) to receive either HBAI20 vaccine or HBVaxPro®‐10 µg in a 0, 1 and 2‐month schedule. The primary outcome was seroprotection (titre ≥ 10 mIU/ml) measured 1‐3 months following the third vaccination.ResultsA total of 133 participants were randomised to receive either HBAI20 vaccine (n = 101) or HBVaxPro®‐10 µg (n = 32). In the modified intention‐to‐treat analysis, the seroprotection rate after the third vaccination was 92.0% (80/87) in the HBAI20 group and 79.3% (23/29) in the HBVaxPro®‐10‐µg group, P = .068. Using a generalised linear mixed model to adjust for stratification factors, a higher odds of seroprotection with HBAI20 vaccine was shown (adjusted odds ratio = 3.48, P = .028). Frequency of mild and moderate local adverse events was greater in the HBAI20 group than in the HBVaxPro®‐10 µg. Rates of severe local adverse events and systemic adverse events were low and similar in both groups.ConclusionsIn this group of hepatitis B vaccine non‐responders, the HBAI20 vaccine demonstrated a higher seroprotection rate when adjusting for stratification factors and a similar safety profile compared to the licensed recombinant HBVaxPro®‐10 µg.
“Everything is not everywhere”: Time‐calibrated phylogeography of the genus Milnesium (Tardigrada)
Authors: Morek Witold , Surmacz Bartłomiej , López‐López Alejandro , Michalczyk Łukasz 
Published: May 2021

AbstractThere is ample evidence that macroscopic animals form geographic clusters termed as zoogeographic realms, whereas distributions of species of microscopic animals are still poorly understood. The common view has been that micrometazoans, thanks to their putatively excellent dispersal abilities, are subject to the “Everything is everywhere but environment selects” hypothesis (EiE). One of such groups, <1 mm in length, are limnoterrestrial water bears (Tardigrada), which can additionally enter cryptobiosis that should further enhance their potential for long distance dispersion (e.g., by wind). However, an increasing number of studies, including the most recent phylogeny of the eutardigrade genus Milnesium, seem to question the general applicability of the EiE hypothesis to tardigrade species. Nevertheless, all Milnesium phylogenies published to date were based on a limited number of populations, which are likely to falsely suggest limited geographic ranges. Thus, in order to test the EiE hypothesis more confidently, we considerably enlarged the Milnesium data set both taxonomically and geographically, and analysed it in tandem with climate type and reproductive mode. Additionally, we time‐calibrated our phylogeny to align it with major geological events. Our results show that, although cases of long distance dispersal are present, they seem to be rare and mostly ancient. Overall, Milnesium species are restricted to single zoogeographic realms, which suggests that these tardigrades have limited dispersal abilities. Finally, our results also suggest that the breakdown of Gondwana may have influenced the evolutionary history of Milnesium. In conclusion, phylogenetic relationships within the genus seem to be determined mainly by paleogeography.
Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium ‘fitti’) among closely related coral hosts
Authors: Reich Hannah G. , Kitchen Sheila A. , Stankiewicz Kathryn H. , Devlin‐Durante Meghann , Fogarty Nicole D. , Baums Iliana B. 
Published: May 2021

AbstractMutualisms where hosts are coupled metabolically to their symbionts often exhibit high partner fidelity. Most reef‐building coral species form obligate symbioses with a specific species of photosymbionts, dinoflagellates in the family Symbiodiniaceae, despite needing to acquire symbionts early in their development from environmental sources. Three Caribbean acroporids (Acropora palmata,A. cervicornisand their F1hybrid) are sympatric across much of their range, but often occupy different depth and light habitats. Throughout this range, both species and their hybrid associate with the endosymbiotic dinoflagellateSymbiodinium‘fitti’. Because light (and therefore depth) influences the physiology of dinoflagellates, we investigated whetherS. ‘fitti’ populations from each host taxon were differentiated genetically. Single nucleotide polymorphisms (SNPs) amongS. ‘fitti’ strains were identified by aligning shallow metagenomic sequences of acroporid colonies sampled from across the Caribbean to a ~600‐Mb draft assembly of theS. ‘fitti’ genome (from the CFL14120A. cervicornismetagenome). Phylogenomic and multivariate analyses revealed that genomic variation amongS. ‘fitti’ strains partitioned to each host taxon rather than by biogeographical origin. This is particularly noteworthy because the hybrid has a sparse fossil record and may be of relatively recent origin. A subset (37.6%) of the SNPs putatively under selection were nonsynonymous mutations predicted to alter protein efficiency. Differences in genomic variation ofS. ‘fitti’ strains from each host taxon may reflect the unique selection pressures created by the microenvironments associated with each host. The nonrandom sorting amongS. ‘fitti’ strains to different hosts could be the basis for lineage diversification via disruptive selection, leading to ecological specialization and ultimately speciation.
Blockchain technology and smart contract for civil structural health monitoring system
Authors: Xu Jie , Liu Haoran , Han Qinghua 
Published: May 2021

AbstractThe rapid development of blockchain technology is exerting a profound impact on all walks of life. Blockchain, which is a decentralized and distributed technology architecture, has inspired people to think about the social development model. However, blockchain technology has not been applied to health monitoring. Therefore, this study proposes a distributed health monitoring system based on blockchain technology, which realizes data security, information transparency, efficient sharing, and independent decision making with smart contracts. First, the system is designed as a blockchain network for structural health monitoring (SHM), and a series of smart contracts for health monitoring is developed to achieve monitoring authority verification, structural damage identification, and other functions. Based on the strength of the Ethereum private chain and Guangzhou New TV Tower benchmark model, smart contracts for health monitoring were deployed, and a series of tests of the proposed system were performed. The results indicate that the proposed system can provide monitoring authority verification, generate abnormal alerts, immutability of data, attack resistance, and traceability query.