bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)
Authors: Tang Boping , Zhang Daizhen , Li Haorong , Jiang Senhao , Zhang Huabin , Xuan Fujun , Ge Baoming , Wang Zhengfei , Liu Yu , Sha Zhongli , Cheng Yongxu , Jiang Wei , Jiang Hui , Wang Zhongkai , Wang Kun , Li Chaofeng , Sun Yue , She Shusheng , Qiu Qiang , Wang Wen , Li Xinzheng , Li Yongxin , Liu Qiuning , Ren Yandong 
Published: January 2020

Abstract

Background
The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking.

Findings
Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology.

Conclusions
We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.
A fast algorithm for multiple elimination and transmission compensation in primary reflections
Authors: Zhang Lele , Slob Evert 
Published: January 2020

SUMMARY
The transmission compensated primary reflections can be obtained from the single-sided acoustic reflection response in the two-way traveltime domain. This is achieved by eliminating free-surface and internal multiple reflections and compensating for transmission losses in primary reflections without model information. The substantial computational cost of the proposed scheme can be reduced by an order of magnitude with a fast implementation version. This is achieved by using the previously computed filter functions as initial estimate for every new truncation time value. We evaluate the success of the scheme with simple and complex 2-D numerical examples. We find that the scheme has excellent performance in most cases, except for the case where strong reflectors are present. In such case, the current scheme suffers from lack of convergence.
Analytic solutions for calcium ion fertilisation waves on the surface of eggs – erratum
Authors: Bradshaw-Hajek Bronwyn H , Broadbridge Philip 
Published: January 2020

Abstract
The paper, “Analytic solutions for calcium ion fertilisation waves on the surface of eggs” by the current authors (this journal 2019), adopted an incorrect solution to Legendre’s equation that had been tabulated in a well known compendium of solutions of differential equations. The solution to the linear equation and the consequent solution of the considered nonlinear problem, are corrected here. The solution maintains the same character and the conclusions are the same. Numerical evaluations and graphic outputs have been modified.
Serum Free Light Chain Assay: Shift Toward a Higher κ/λ Ratio
Authors: Rindlisbacher Barbara , Schild Christof , Egger Florence , Bacher Vera U , Pabst Thomas , Leichtle Alexander , Andres Martin , Sédille-Mostafaie Nazanin 
Published: January 2020

AbstractBackgroundThe analysis of serum free light chains (FLCs) is clinically relevant for the diagnosis and therapeutic management of clonal plasma cell disorders. This study compares the performance of monoclonal and polyclonal FLC κ and λ assays in clinical samples determined in a single academic center.MethodsSerum FLCs were analyzed from 102 patients using the Freelite (Binding Site) and N Latex (Siemens) assays on the BN ProSpec System (Siemens). When available, data for protein electrophoresis, immunofixation, C-reactive protein, and estimated glomerular filtration rate (eGFR) were combined with FLC results to evaluate performance.ResultsMethod evaluation showed acceptable imprecision and inaccuracy measures of &lt;4.4% and 12.9%, respectively. Poor agreement between the methods was observed, including constant and proportional bias and poor correlation (Kendall τ, 0.671–0.901). The N Latex assay was not affected by the renal impairment estimated by eGFR, unlike the FLC κ/λ ratio results by the Freelite assay. With the Freelite assay, 98% of putative controls without monoclonal gammopathy (n = 42) showed a κ/λ ratio that was above the median of the standard diagnostic range or renal diagnostic range. A shift toward higher κ/λ ratios was also observed when retrospective data between 2011 and 2017 were compared.ConclusionsUnlike the Freelite assay, κ/λ ratios analyzed with the N Latex assay were not affected by renal failure. Both methods showed acceptable performances using nephelometry, but they were poorly correlated. A shift toward κ/λ ratios might impair the specificity of borderline increased κ/λ results. This should be considered when interpreting FLC κ and λ results.
Acceptability of smartphone applications for facilitating layperson naloxone administration during opioid overdoses
Authors: Marcu Gabriela , Aizen Roy , Roth Alexis M , Lankenau Stephen , Schwartz David G 
Published: January 2020

Abstract

Objective
We investigated user requirements for a smartphone application to coordinate layperson administration of naloxone during an opioid overdose.

Materials and Methods
We conducted interviews and focus groups with 19 nonmedical opioid users and other community members in the Kensington neighborhood of Philadelphia, Pennsylvania, which has one of the highest overdose rates in the country. Data were analyzed using thematic analysis.

Results
We found high levels of trust and reliance within one’s own social group, especially nonmedical opioid users and members of the neighborhood. Participants distrusted outsiders, including professional responders, whom they perceived as uncaring and prejudiced. Participants expressed some concern over malicious use of a location-based application, such as theft when a victim is unconscious, but overall felt the benefits could outweigh the risks. Participants also trusted community-based organizations providing services such as bystander training and naloxone distribution, and felt that a smartphone application should be integrated into these services.

Discussion
Individuals affected by opioid use and overdose reacted positively to the concept for a smartphone application, which they perceived as a useful tool that could help combat the high rate of opioid overdose fatalities in their neighborhood. A sense of unity with others who have shared their experiences could be leveraged to connect willing bystanders with victims of overdose, but risk must be mitigated for layperson responders.

Conclusion
Based on participant experiences with overdoses, trust-based considerations for the design of smartphone applications to facilitate layperson response will be critical for their adoption and use in real overdose situations.
Heritage and genealogy travel health concerns in the era of in-home DNA testing
Authors: Angelo Kristina M , Breiman Jennifer , Wu Henry M , Nemhauser Jeffrey , Walker and Allison T 
Published: January 2020

Highlight
The rise of in-home DNA testing has led to a novel trend in heritage travel, these travelers may be inexperienced and visit areas lacking tourism infrastructure, which may put them at higher risk of infection and injury. Healthcare providers must identify heritage travelers and inform them about travel-associated health risks.
Cut elimination and complexity bounds for intuitionistic epistemic logic
Authors: Krupski Vladimir N 
Published: January 2020

Abstract
The formal system of intuitionistic epistemic logic (IEL) was proposed by S. Artemov and T. Protopopescu. It provides the formal foundation for the study of knowledge from an intuitionistic point of view based on Brouwer–Heyting–Kolmogorov semantics of intuitionism. We construct a cut-free sequent calculus for IEL and establish that polynomial space is sufficient for the proof search in it. We prove that IEL is PSPACE-complete.
Emission peaks in the light curve of core collapse supernovae by late jets
Authors: Kaplan Noa , Soker Noam 
Published: January 2020

ABSTRACT
We build a toy model where the central object, i.e. a newly born neutron star or a black hole, launches jets at late times and show that these jets might account for peaks in the light curve of some peculiar (i.e. having unusual light curves) core collapse supernovae (CCSNe) when the jets interact with the CCSN ejecta. We assume that the central object accretes fallback material and launches two short-lived opposite jets weeks to months after the explosion. We model each jet-ejecta interaction as a spherically symmetric ‘mini-explosion’ that takes place inside the ejecta. We assume that each ‘mini-explosion’ adds emission that is symmetric in time around the late peak, and with a rise in emission power that has the same slope as that of the main CCSN light curve. In total, we use 12 parameters in the toy model. In our toy model, late jets form stronger emission peaks than early jets. Late jets with a kinetic energy of only about one per cent of the kinetic energy of the CCSN itself might form strong emission peaks. We apply our toy model to the brightest peak of the enigmatic CCSN iPTF14hls that has several extra peaks in its light curve. We can fit this emission peak with our toy model when we take the kinetic energy of the jets to be about 1–2 per cent of the CCSN energy, and the shocked ejecta mass to be about 3 per cent of the ejecta mass.
Validity of Algorithms for Identification of Individuals Suffering from Chronic Noncancer Pain in Administrative Databases: A Systematic Review
Authors: Lacasse Anaïs , Cauvier Charest Elizabeth , Dault Roxanne , Cloutier Anne-Marie , Choinière Manon , Blais Lucie , Vanasse Alain 
Published: January 2020

AbstractBackgroundSecondary analysis of health administrative databases is indispensable to enriching our understanding of health trajectories, health care utilization, and real-world risks and benefits of drugs among large populations.ObjectivesThis systematic review aimed at assessing evidence about the validity of algorithms for the identification of individuals suffering from nonarthritic chronic noncancer pain (CNCP) in administrative databases.MethodsStudies reporting measures of diagnostic accuracy of such algorithms and published in English or French were searched in the Medline, Embase, CINAHL, AgeLine, PsycINFO, and Abstracts in Social Gerontology electronic databases without any dates of coverage restrictions up to March 1, 2018. Reference lists of included studies were also screened for additional publications.ResultsOnly six studies focused on commonly studied CNCP conditions and were included in the review. Some algorithms showed a ≥60% combination of sensitivity and specificity values (back pain disorders in general, fibromyalgia, low back pain, migraine, neck/back problems studied together). Only algorithms designed to identify fibromyalgia cases reached a ≥80% combination (without replication of findings in other studies/databases).ConclusionsIn summary, the present investigation informs us about the limited amount of literature available to guide and support the use of administrative databases as valid sources of data for research on CNCP. Considering the added value of such data sources, the important research gaps identified in this innovative review provide important directions for future research. The review protocol was registered with PROSPERO (CRD42018086402).
Dynamical breaking to special or regular subgroups in the SO(N) Nambu–Jona-Lasinio model
Authors: Kugo Taichiro , Yamatsu Naoki 
Published: January 2020

Abstract
It was recently shown that in four-dimensional $SU(N)$ Nambu–Jona-Lasinio (NJL) type models, the $SU(N)$ symmetry breaking into its special subgroups is not special but much more common than that into the regular subgroups, where the fermions belong to complex representations of $SU(N)$. We perform the same analysis for the $SO(N)$ NJL model for various $N$ with fermions belonging to an irreducible spinor representation of $SO(N)$. We find that the symmetry breaking into special or regular subgroups has some correlation with the type of fermion representations; i.e. complex, real, pseudo-real representations.
Intranasal dexmedetomidine premedication in children with recent upper respiratory tract infection undergoing interventional cardiac catheterisation
Authors: Zhang Sen , Zhang Ruidong , Cai Meihua , Zhang Kan , Zhang Mazhong , Zheng Jijian 
Published: January 2020

BACKGROUND
Recent upper respiratory tract infection (URI) is a risk factor for the occurrence of peri-operative respiratory adverse events (PRAE). This risk may be higher in children with congenital heart disease (CHD), particularly in those undergoing interventional cardiac catheterisation. It is therefore essential to adapt the anaesthetic strategy in these children to prevent from the occurrence of PRAE.

OBJECTIVE
To determine whether intranasal dexmedetomidine (DEX) premedication can reduce the incidence of PRAE in children with recent URI undergoing interventional cardiac catheterisation.

DESIGN
Randomised controlled trial.

SETTING
Single-centre study based at a tertiary care centre in Shanghai, China.

PATIENTS
A total of 134 children with CHD aged 0 to 16 years with recent URI undergoing interventional cardiac catheterisation.

INTERVENTIONS
Children were randomised to receive either intranasal DEX 1.5 μg kg−1 (DEX group) or intranasal saline (Placebo group) 30 to 45 min before anaesthesia induction.

MAIN OUTCOME MEASURES
The incidence of PRAE.

RESULTS
Intranasal DEX significantly reduced the incidence of PRAE (P = 0.001), particularly oxygen desaturation (P = 0.012). Most PRAE were observed during the emergence phase. The incidence of PRAE was comparable among the three types of left–right shunt CHD children in both groups. In children aged less than 3 years, the incidence of PRAE was significantly lower in the DEX group (P = 0.003). In contrast, the incidence of PRAE was comparable between the two groups in children aged at least 3 years. No differences in the incidence of emergence agitation, fever and vomiting between the two groups were noted.

CONCLUSION
Administration of intranasal DEX 1.5 μg kg−1 30 to 45 min before induction led to a reduction in the incidence of PRAE in children aged less than 3 years with recent URI undergoing interventional cardiac catheterisation.

TRIAL REGISTRATION
chictr.org.cn identifier: ChiCTR-RRC-17012519.
A synthesis and meta-analysis of the Fe chemistry of serpentinites and serpentine minerals
Authors: Mayhew Lisa E. , Ellison Eric T. 
Published: January 2020

The iron chemistry of serpentinites and serpentine group minerals is often invoked as a record of the setting and conditions of serpentinization because Fe behaviour is influenced by reaction conditions. Iron can be partitioned into a variety of secondary mineral phases and undergo variable extents of oxidation and/or reduction during serpentinization. This behaviour influences geophysical, geochemical and biological aspects of serpentinizing systems and, more broadly, earth systems. Iron chemistry of serpentinites and serpentines is frequently analysed and reported for single systems. Interpretations of the controls on, and the implications of, Fe behaviour drawn from a single system are often widely extrapolated. There is a wealth of serpentinite/serpentine chemical composition data available in the literature. Consequently, compilation of a database including potential predictors of Fe behaviour and measures of Fe chemistry enables systematic investigation of trends in Fe behaviour across a variety of systems and conditions. The database presented here contains approximately 2000 individual data points including both bulk rock and serpentine mineral geochemical data which are paired whenever possible. Measures of total Fe and Fe oxidation state, which are more limited, are compiled with characteristics of the systems from which they were sampled. Observations of trends in Fe chemistry in serpentinites and serpentines across the variety of geologic systems and parameters will aid in verifying and strengthening interpretations made on the basis of Fe chemistry.
This article is part of a discussion meeting issue ‘Serpentinite in the Earth system’.
The comparable strategic flexibility of model-free and model-based learning
Authors: Filipowicz Alexandre L. S. , Levine Jonathan , Piasini Eugenio , Tavoni Gaia , Kable Joseph W. , Gold Joshua I. 
Published: January 2020

AbstractDifferent learning strategies are thought to fall along a continuum that ranges from simple, inflexible, and fast “model-free” strategies, to more complex, flexible, and deliberative “model-based strategies”. Here we show that, contrary to this proposal, strategies at both ends of this continuum can be equally flexible, effective, and time-intensive. We analyzed behavior of adult human subjects performing a canonical learning task used to distinguish between model-free and model-based strategies. Subjects using either strategy showed similarly high information complexity, a measure of strategic flexibility, and comparable accuracy and response times. This similarity was apparent despite the generally higher computational complexity of model-based algorithms and fundamental differences in how each strategy learned: model-free learning was driven primarily by observed past responses, whereas model-based learning was driven primarily by inferences about latent task features. Thus, model-free and model-based learning differ in the information they use to learn but can support comparably flexible behavior.Statement of RelevanceThe distinction between model-free and model-based learning is an influential framework that has been used extensively to understand individual- and task-dependent differences in learning by both healthy and clinical populations. A common interpretation of this distinction that model-based strategies are more complex and therefore more flexible than model-free strategies. However, this interpretation conflates computational complexity, which relates to processing resources and generally higher for model-based algorithms, with information complexity, which reflects flexibility but has rarely been measured. Here we use a metric of information complexity to demonstrate that, contrary to this interpretation, model-free and model-based strategies can be equally flexible, effective, and time-intensive and are better distinguished by the nature of the information from which they learn. Our results counter common interpretations of model-free versus model-based learning and demonstrate the general usefulness of information complexity for assessing different forms of strategic flexibility.
Host environmental conditions induce small fungal cell size and alter population heterogeneity in Cryptococcus neoformans
Authors: Zhou Xin , Zafar Hanna , Sephton-Clark Poppy , Mohamed Sally H. , Chapuis Ambre , Makarova Maria , MacCallum Donna M. , Drummond Rebecca A. , Dambuza Ivy M. , Ballou Elizabeth R. 
Published: January 2020

AbstractFungal morphology significantly impacts the host response. Filamentation and tissue penetration by Candida and Aspergillus species are essential for virulence, while growth as a yeast allows the thermal dimorphic fungi Coccidiodes, Histoplasma, and Talaromyces to reside inside phagocytes and disseminate. The basidiomycete Cryptococcus neoformans exhibits an unusual yeast-to-titan transition thought to enhance pathogenicity by increasing fungal survival in the host lung and dissemination to the central nervous system. In a common laboratory strain (H99), in vitro and in vivo titan induction yields a heterogenous population including >10 μm titan cells, 5-7 μm yeast cells and 2-4 μm titanides. Previous reports have shown that titan cells are associated with enhanced virulence and the generation of aneuploid cells that facilitate stress adaptation and drug resistance, while small (>10 μm) cells are associated with increased dissemination. However, the relationship between titan cells, small cells, and titanides remains unclear. Here, we characterize titanides and small cells in H99 and three clinical isolates and show that titanides share the lipid membrane order of their titan mothers and the G0 quiescent-like DNA staining of mating spores. In addition, we show that both titanizing and non-titanizing isolates exhibit altered capsule structure and PAMP exposure over time during in vitro culture, and generate aneuploidy in vivo.Author summaryThe human fungal pathogen Cryptococcus neoformans causes 200,000 HIV-associated deaths each year. In the lung, Cryptococcus makes an unusual yeast-to-titan morphological switch that contributes to disease development by altering immune polarization and introducing aneuploidy underlying host stress and drug resistance. Specifically, a proportion of 5 um haploid yeast endoreduplicate and swell, converting to large (> 10 um) polyploid titan cells that can then produce genetically distinct daughter cells. We recently developed an in vitro protocol for inducing large titan cells and additionally observed a novel small “titanide” cell type. Here we investigate the nature and origin of these small cells, demonstrating that they emerge during both in vitro and in vivo mouse-passaged titan induction in the well characterised lab strain H99 and are also apparent in a titanizing clinical isolate, Zc8. We show that these titanide cells share features with titan mothers (lipid order) and with spores produced during heterothalic mating. Finally, we show that the capacity of clinical isolates to produce both titan and titanide cells impacts aneuploidy and the emergence of drug resistance in vivo.
Subpopulations of sensorless bacteria drive fitness in fluctuating environments
Authors: Julou Thomas , Zweifel Ludovit , Blank Diana , Fiori Athos , van Nimwegen Erik 
Published: January 2020

AbstractPopulations of bacteria often undergo a lag in growth when switching conditions. Because growth lags can be large compared to typical doubling times, variations in growth lag are an important but often overlooked component of bacterial fitness in fluctuating environments. We here explore how growth lag variation is determined for the archetypical switch from glucose to lactose as a carbon source inE. coli. First, we show that single-cell lags are bimodally distributed and controlled by a single-molecule trigger. That is, gene expression noise causes the population before the switch to divide cells with zero pre-existing into subpopulations with zero and nonzerolacoperon expression. While ’sensorless’lacexpression at the switch have long lags because they are unable to sense the lactose signal, any nonzerolacoperon expression suffices to ensure a short lag. Second, we show that the growth lag at the population level depends crucially on the fraction of sensorless cells, and that this fraction in turn depends sensitively on the growth condition before the switch. Consequently, even small changes in basal expression affecting the fraction of sensorless cells can significantly affect population lags and fitness under switching conditions, and may thus be subject to significant natural selection. Indeed, we show that condition-dependent population lags vary across wildE. coliisolates. Since many sensory genes are naturally low expressed in conditions where their inducer is not present, bimodal responses due to subpopulations of sensorless cells may be a general mechanism inducing phenotypic heterogeneity and controlling population lags in switching environments. This mechanism also illustrates how gene expression noise can turn even simple sensory gene circuits into a bet-hedging module, and underlines the profound role of gene expression noise in regulatory responses.