bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle
Authors: Xuan Biao , Park Jongbin , Choi Sukjung , You Inhwan , Nam Bo-Hye , Noh Eun Soo , Kim Eun Mi , Song Mi-Young , Shin Younhee , Jeon Ji-Hyeon , Kim Eun Bae 
Published: May 2021

Abstract
Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species and a winter economic aquaculture resource in South Korea. Because of its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summers. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) vs. warm (HT, 23°C) conditions to identify heat stress–induced genes and gene categories. We observed a total of 1987 contigs with N50 of 0.46 Mbp, with the largest contig (3.03 Mbp) in the assembled genome. A total of 20,644 protein-coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology terms and 11,560 genes for KEGG Orthology. We conducted the lost and gained genes analysis compared with three species that: human, zebrafish, and salmon. In the lost genes analysis, we detected that smelt lost 4461 (22.16%), 2825 (10.62%), and 1499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed that smelt gained 1133 (5.49%), 1670 (8.09%), and 229 (1.11%) genes compared with the above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with a false discovery rate &lt;0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that upregulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P &lt; 0.001) and regulation of apoptotic process (GO:0042981, P &lt; 0.01), and genes were downregulated by immune responses such as myeloid cell differentiation (GO:0030099, P &lt; 0.001) in the liver under heat stress. In muscle tissue, upregulated genes were enriched for hypoxia (GO:0001666, P &lt; 0.05), transcription regulator activity (GO:0140110, P &lt; 0.001), and calcium-release channel activity (GO:0015278, P &lt; 0.01), and genes were downregulated for a nicotinamide nucleotide biosynthetic process (GO:0019359, P &lt; 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of molecular mechanisms and heat responses and be useful for predicting survival of the smelt and its closely related species under global warming.
The Role of Media Sources for COVID-19 Information on Engaging in Recommended Preventive Behaviors Among Medicare Beneficiaries Aged ≥ 65 Years
Authors: Ng Boon Peng , Park Chanhyun 
Published: May 2021

Abstract

Objectives
The public relies on various media sources and communication platforms for receipt of coronavirus disease 2019 (COVID-19) information. Therefore, identifying the primary sources of COVID-19 information among older adults can be valuable, as it can enable information on life-saving measures to be effectively disseminated to this population.

Methods
We analyzed the Medicare Current Beneficiary Survey COVID-19 Supplement that was administrated from June 2020 through July 2020 (n = 8,050). A survey-weighted logistic model was conducted to examine the association between the sources of COVID-19 information Medicare beneficiaries most relied on (i.e., traditional news sources, social media, comments/guidance from government officials, other webpages/internet, friends/family members, and health care providers) and engaging in all 3 recommended preventive behaviors (i.e., mask wearing, social distancing, and handwashing).

Results
Among study participants, 89.8% engaged in all 3 recommended preventive behaviors. Approximately 59.3% of beneficiaries reported that they most relied upon traditional news sources for COVID-19 information; 11.4% reported health care providers; 10.6% reported comments/guidance from government officials; 8.8% reported other webpages/internet; 8.6% reported friends/family members; and 1.3% reported they relied upon social media. Beneficiaries who relied on comments/guidance from government officials for COVID-19 information (vs. traditional news sources) were more likely to engage in preventive behaviors (odds ratio [OR] = 1.68, 95% confidence interval [CI] = 1.20–2.35). However, those who relied on COVID-19 information from friends/family members (vs. traditional news sources) were less likely to engage in preventive behaviors (OR = 0.56, 95% CI = 0.44–0.73).

Discussion
Our findings can inform decision making about the effective communication sources to reach Medicare beneficiaries for public health messaging regarding preventive measures, including COVID-19 vaccination.
Using Task Models to Understand the Intersection of Numeracy Skills and Technical Competence With Medical Device Design
Authors: Bowen Judy , Coben Diana 
Published: May 2021

AbstractTask models are used in many different ways throughout the design and development of interactive systems. When the interactive systems are safety critical, task models can play an important role in ensuring system behaviours are consistent with user requirements, which may help to prevent errors. While task models can be used to describe a user’s goals and the steps required to achieve that goal, to understand where user errors may occur we also need to consider the users’ understanding of how to perform a task and how this relates to the system they are using. Our focus is on the use of medical devices such as syringe drivers and infusion pumps for intravenous medication, which forms a major part of hospital inpatient care throughout the world. While we might rely on software engineering and human factors techniques to ensure correctness of such devices, their use by medical personnel in practice includes other factors that are equally important. These include training medical personnel in the use of medical devices. Also numeracy education for medical staff to ensure that they are able to set up and perform the necessary calculations to convert prescribed medication into the appropriate values and measures for their delivery mechanisms. We have developed an approach that aims to bring together concepts of technology design (both functional correctness and usability concerns), numeracy and medication delivery competency. In order to do so we use task models as a common language that enables us to consider these different domains in a single way. We find that the ability to describe the two domains within a single process allows us to compare models of knowledge, tasks and use of devices, which can elicit potential mismatches and problems.
Education: An introduction to the core data for cefiderocol with reflections for a possible role within UK clinical practice
Authors: Karas J Andreas , Edgeworth Jonathan 
Published: May 2021

Abstract
The video in this section is a copy of a recorded webinar organized by Shionogi to launch cefiderocol to the UK market in September 2020. Dr Andreas Karas presents the key clinical data for this new antibiotic for MDR Gram-negative infections, followed by reflections from Professor Jonathan Edgeworth on the potential use of the new agent in UK clinical practice. Included in the latter is a case study example of a compassionate use case using cefiderocol. The prescribing information for cefiderocol is available at: https://shionogi-eu-content.com/gb/fetcroja/pi.
Water quality associations and spatiotemporal distribution of the harmful alga Prymnesium parvum in an impounded urban stream system
Authors: Clayton John B , Patiño Reynaldo , Rashel Rakib H , Tábora-Sarmiento Shisbeth 
Published: May 2021

Abstract
The Jim Bertram Lake System consists of several stream impoundments within the City of Lubbock, Texas (USA). Baseflow in the upstream reach is dominated by nitrogen-rich-treated wastewater. While toxic blooms of Prymnesium parvum have occurred in this system for ∼2 decades during fall or winter-spring, little is known about water quality variables that facilitate blooms or the alga’s spatiotemporal distribution. Water quality associations were examined monthly over a 1-year period. Total phosphorus was largely below the detection limit, suggesting that the system is phosphorus limited. Algal abundance was low during the assessment period and associations were determined using multiple logistic regression. Algal incidence was negatively associated with temperature and positively with organic nitrogen and calcium hardness. These findings conform with earlier reports but positive associations with the latter two variables are noteworthy because they have not been widely confirmed. Spatiotemporal distribution was evaluated in fall and winter-spring of three consecutive years. Prymnesium parvum incidence was higher in the upper than in the lower reach, and detections in the lower reach occurred only after a dense bloom developed in the upper reach contemporaneously with stormwater runoff-associated flooding. Thus, the upstream reach is a major source of propagules for downstream sites. Because urban runoff is a source of phosphorus and its nitrogen: phosphorus ratio is lower than prevailing ratios in the upper reach, what triggered the bloom was likely relief from phosphorus limitation. This study provided water quality, geographic and hydrological indices that may inform prevention and control methods for harmful algae in nitrogen-enriched urban systems.
The complex variability of blazars: time-scales and periodicity analysis in S4 0954+65
Authors: Raiteri C M , Villata M , Larionov V M , Jorstad S G , Marscher A P , Weaver Z R , Acosta-Pulido J A , Agudo I , Andreeva T , Arkharov A , Bachev R , Benítez E , Berton M , Björklund I , Borman G A , Bozhilov V , Carnerero M I , Carosati D , Casadio C , Chen W P , Damljanovic G , D’Ammando F , Escudero J , Fuentes A , Giroletti M , Grishina T S , Gupta A C , Hagen-Thorn V A , Hart M , Hiriart D , Hou W-J , Ivanov D , Kim J-Y , Kimeridze G N , Konstantopoulou C , Kopatskaya E N , Kurtanidze O M , Kurtanidze S O , Lähteenmäki A , Larionova E G , Larionova L V , Marchili N , Markovic G , Minev M , Morozova D A , Myserlis I , Nakamura M , Nikiforova A A , Nikolashvili M G , Otero-Santos J , Ovcharov E , Pursimo T , Rahimov I , Righini S , Sakamoto T , Savchenko S S , Semkov E H , Shakhovskoy D , Sigua L A , Stojanovic M , Strigachev A , Thum C , Tornikoski M , Traianou E , Troitskaya Y V , Troitskiy I S , Tsai A , Valcheva A , Vasilyev A A , Vince O , Zaharieva E 
Published: May 2021

ABSTRACT
Among active galactic nuclei, blazars show extreme variability properties. We here investigate the case of the BL Lac object S4 0954+65 with data acquired in 2019–2020 by the Transiting Exoplanet Survey Satellite (TESS) and by the Whole Earth Blazar Telescope (WEBT) Collaboration. The 2-min cadence optical light curves provided by TESS during three observing sectors of nearly 1 month each allow us to study the fast variability in great detail. We identify several characteristic short-term time-scales, ranging from a few hours to a few days. However, these are not persistent, as they differ in the various TESS sectors. The long-term photometric and polarimetric optical and radio monitoring undertaken by the WEBT brings significant additional information, revealing that (i) in the optical, long-term flux changes are almost achromatic, while the short-term ones are strongly chromatic; (ii) the radio flux variations at 37 GHz follow those in the optical with a delay of about 3 weeks; (iii) the range of variation of the polarization degree and angle is much larger in the optical than in the radio band, but the mean polarization angles are similar; (iv) the optical long-term variability is characterized by a quasi-periodicity of about 1 month. We explain the source behaviour in terms of a rotating inhomogeneous helical jet, whose pitch angle can change in time.
Survival of ALMA rings in the absence of pressure maxima
Authors: Jiang (蒋昊昌) Haochang , Ormel Chris W 
Published: May 2021

ABSTRACT
Recent ALMA observations have revealed that a large fraction of protoplanetary discs contain bright rings at (sub)millimetre wavelengths. Dust trapping induced by pressure maxima in the gas disc is a popular explanation for these rings. However, it is unclear whether such pressure bumps can survive for evolutionary time-scales of the disc. In this work, we investigate an alternative scenario, which involves only dust–gas interactions in a smooth gas disc. We postulate that ALMA rings are a manifestation of a dense, clumpy mid-plane that is actively forming planetesimals. The clumpy medium itself hardly experiences radial drift, but clumps lose mass by disintegration and vertical transport and planetesimal formation. Starting from a seed ring, we numerically solve the transport equations to investigate the ring’s survival. In general, rings move outwards due to diffusion of the clump component. Without pressure support, rings leak material at rates ∼40 ${\rm M}_\oplus \, \mathrm{Myr}^{-1}$ and in order for rings to survive, they must feed from an external mass reservoir of pebbles. In the case where the pebble size is constant in the disc, a cycle between ring formation and dispersion emerges. Rings produce large quantities of planetesimals, which could be material for planet formation and explain the massive budget inferred debris disc. Mock images of ALMA observations compare well to the rings of Elias 24 and AS 209 from DSHARP’s sample.
AT2017gfo: Bayesian inference and model selection of multicomponent kilonovae and constraints on the neutron star equation of state
Authors: Breschi Matteo , Perego Albino , Bernuzzi Sebastiano , Del Pozzo Walter , Nedora Vsevolod , Radice David , Vescovi Diego 
Published: May 2021

ABSTRACTThe joint detection of the gravitational wave GW170817, of the short γ-ray burst GRB170817A and of the kilonova AT2017gfo, generated by the the binary neutron star (NS) merger observed on 2017 August 17, is a milestone in multimessenger astronomy and provides new constraints on the NS equation of state. We perform Bayesian inference and model selection on AT2017gfo using semi-analytical, multicomponents models that also account for non-spherical ejecta. Observational data favour anisotropic geometries to spherically symmetric profiles, with a log-Bayes’ factor of ∼104, and favour multicomponent models against single-component ones. The best-fitting model is an anisotropic three-component composed of dynamical ejecta plus neutrino and viscous winds. Using the dynamical ejecta parameters inferred from the best-fitting model and numerical–relativity relations connecting the ejecta properties to the binary properties, we constrain the binary mass ratio to q &lt; 1.54 and the reduced tidal parameter to $120\lt \tilde{\Lambda }\lt 1110$. Finally, we combine the predictions from AT2017gfo with those from GW170817, constraining the radius of a NS of 1.4 M⊙ to 12.2 ± 0.5 km (1σ level). This prediction could be further strengthened by improving kilonova models with numerical-relativity information.
Neuro-Oncology PracticeClinical Debate: FDG PET to differentiate glioblastoma recurrence from treatment-related changes
Authors: Parent Ephraim E , Johnson Derek R , Gleason Tyler , Villanueva-Meyer Javier E 
Published: May 2021

AbstractThe ability to accurately differentiate treatment-related changes (ie, pseudoprogression and radiation necrosis) from recurrent glioma remains a critical diagnostic problem in neuro-oncology. Because these entities are treated differently and have vastly different outcomes, accurate diagnosis is necessary to provide optimal patient care. In current practice, this diagnostic quandary commonly requires either serial imaging or histopathologic tissue confirmation. In this article, experts in the field debate the utility of 2-deoxy-2[18F]fluoro-d-glucose positron emission tomography (FDG PET) as an imaging tool to distinguish tumor recurrence from treatment-related changes in a patient with glioblastoma and progressive contrast enhancement on magnetic resonance (MR) following chemoradiotherapy.
Next-Generation Sequencing to Detect Pathogens in Pediatric Febrile Neutropenia: A Single-Center Retrospective Study of 112 Cases
Authors: Horiba Kazuhiro , Torii Yuka , Okumura Toshihiko , Takeuchi Suguru , Suzuki Takako , Kawada Jun-ichi , Muramatsu Hideki , Takahashi Yoshiyuki , Ogi Tomoo , Ito Yoshinori 
Published: May 2021

Abstract

Background
Febrile neutropenia (FN) is a frequent complication in immunocompromised patients. However, causative microorganisms are detected in only 10% of patients. This study aimed to detect the microorganisms that cause FN using next-generation sequencing (NGS) to identify the genome derived from pathogenic microorganisms in the bloodstream. Here, we implemented a metagenomic approach to comprehensively analyze microorganisms present in clinical samples from patients with FN.

Methods
FN is defined as a neutrophil count &lt;500 cells/µL and fever ≥37.5°C. Plasma/serum samples of 112 pediatric patients with FN and 10 patients with neutropenia without fever (NE) were sequenced by NGS and analyzed by a metagenomic pipeline, PATHDET.

Results
The putative pathogens were detected by NGS in 5 of 10 FN patients with positive blood culture results, 15 of 87 FN patients (17%) with negative blood culture results, and 3 of 8 NE patients. Several bacteria that were common in the oral, skin, and gut flora were commonly detected in blood samples, suggesting translocation of the human microbiota to the bloodstream in the setting of neutropenia. The cluster analysis of the microbiota in blood samples using NGS demonstrated that the representative bacteria of each cluster were mostly consistent with the pathogens in each patient.

Conclusions
NGS technique has great potential for detecting causative pathogens in patients with FN. Cluster analysis, which extracts characteristic microorganisms from a complex microbial population, may be effective to detect pathogens in minute quantities of microbiota, such as those from the bloodstream.
Transforming the Urban Space: Catholic Survival Through Spatial Practices in Post-Reformation Utrecht
Authors: Yasuhira Genji 
Published: May 2021

Abstract
This article argues that historians have underestimated the agency which Catholics, a politico-religious minority within the Dutch Republic, wielded in surviving the Reformed regime in seventeenth-century Utrecht, the main theatre of the confessional struggle between Calvinists and Catholics on Dutch soil. The Reformed public authorities strategically attempted to deprive Catholics of their spaces where they could live as Catholics, claiming that they were being Catholic too publicly even inside their private homes. Catholics, for their part, persisted in practising their faith not only in their houses, but also in public facilities, tactically deploying diverse spatial practices; they continued to use the urban space as they had in medieval times, and newly appropriated that space as they sought to adjust to the early modern environment of confessional coexistence. Through their spatial practices, Catholics not only actively facilitated their Catholic way of life, but also played an indispensable role in transforming Utrecht from a mono-religious medieval city to a multi-confessional early modern city. The Utrecht case thus bears witness to a hitherto neglected, yet surprisingly dynamic agency exercised by politico-religious minorities in shaping an urban landscape of coexistence.
Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation
Authors: Burress Edward D , Muñoz Martha M 
Published: May 2021

AbstractIslands are thought to facilitate adaptive radiation by providing release from competition and predation. Anole lizards are considered a classic example of this phenomenon: different ecological specialists (“ecomorphs”) evolved in the Caribbean Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico), resulting in convergent assemblages that are not observed in mainland Latin America. Yet, the role of islands in facilitating adaptive radiation is more often implied than directly tested, leaving uncertain the role of biogeography in stimulating diversification. Here, we assess the proposed “island effect” on anole diversification using Bayesian phylogenetic comparative methods that explicitly incorporate rate heterogeneity across the tree and demonstrate two cases of would be false positives. We discovered that rates of speciation and morphological evolution of island and mainland anoles are equivalent, implying that islands provide no special context for exceptionally rapid diversification. Likewise, rates of evolution were equivalent between island anoles that arose via in situ versus dispersal-based mechanisms, and we found no evidence for island-specific rates of speciation or morphological evolution. Nonetheless, the origin of Anolis is characterized by a speciation pulse that slowed over time—a classic signature of waning ecological opportunity. Our findings cast doubt on the notion that islands catalyzed the anole adaptive radiation and instead point to a key innovation, adhesive toe pads, which facilitated the exploitation of many arboreal niches sparsely utilized by other iguanian lizards. The selective pressures responsible for arboreal niche diversification differ between islands and the mainland, but the tempo of diversification driven by these discordant processes is indistinguishable. [Anolis; Caribbean; key innovation; morphological evolution; RevBayes; speciation.]