bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato
Authors: Pons Clara , Casals Joan , Palombieri Samuela , Fontanet Lilian , Riccini Alessandro , Rambla Jose Luis , Ruggiero Alessandra , Figás Maria
del Rosario , Plazas Mariola , Koukounaras Athanasios , Picarella Maurizio E , Sulli Maria , Fisher Josef , Ziarsolo Peio , Blanca Jose , Cañizares Joaquin , Cammareri Maria , Vitiello Antonella , Batelli Giorgia , Kanellis Angelos , Brouwer Matthijs , Finkers Richard , Nikoloudis Konstantinos , Soler Salvador , Giuliano Giovanni , Grillo Stephania , Grandillo Silvana , Zamir Dani , Mazzucato Andrea , Causse Mathilde , Díez Maria José , Prohens Jaime , Monforte Antonio Jose , Granell Antonio 
Published: May 2022

Abstract
The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. Here we report on the evaluation of the largest traditional tomato collection, which includes 1499 accessions from Southern Europe. Analyses of 70 traits revealed a broad range of phenotypic variability with different distributions among countries, with the culinary end use within each country being the main driver of tomato diversification. Furthermore, eight main tomato types (phenoclusters) were defined by integrating phenotypic data, country of origin, and end use. Genome-wide association study (GWAS) meta-analyses identified associations in 211 loci, 159 of which were novel. The multidimensional integration of phenoclusters and the GWAS meta-analysis identified the molecular signatures for each traditional tomato type and indicated that signatures originated from differential combinations of loci, which in some cases converged in the same tomato phenotype. Our results provide a roadmap for studying and exploiting this untapped tomato diversity.
The biochemical and molecular investigation of flower color and scent sheds lights on further genetic modification of ornamental traits in Clivia miniata
Authors: Li Yueqing , Gao Ruifang , Zhang Jia , Wang Yanan , Kong Peiru , Lu Keyu , Adnan   , Liu Meng , Ao Feng , Zhao Chunli , Wang Li , Gao Xiang 
Published: May 2022

Abstract
Clivia miniata is renowned for its evergreen and strap-like leaves, whereas its floral color and scent are lacking diversity. Here, anthocyanin, volatile terpene, and carotenoid metabolisms were integrally investigated in C. miniata flowers. The results showed that pelargonidins and lutein might cooperate to confer orange or yellow color to C. miniata flowers, but only a trace amount of (+)-limonene was detected. The expression levels of CmF3′H and CmDFR appeared to be responsible for the ratio of cyanidin and pelargonidin derivatives in C. miniata, and the low expression of CmF3′H was responsible for the lack of cyanidins in flowers. Moreover, the CmF3′H promoter could not be activated by CmMYBAs, suggesting that it was controlled by novel regulators. Only two CmTPSs were functional, with CmTPS2 responsible for (+)-limonene synthesis, contributing to the monotonous flower volatile terpenes of C. miniata. CmCCD1a and CmCCD1b were able to cleave carotenoids at the 5,6 (5′,6′), and 9,10 (9′,10′) positions to generate volatile apocarotenoids, whereas the substrates found in low-quantities or specific subcellular localizations of CmCCD1s might constrain volatile apocarotenoid release. Consequently, activating F3′H and introducing novel F3′5′H or versatile TPS may be effective ways to modify the floral color and scent, respectively. Alternatively, modifying the carotenoid flux or CCD1 localization might affect floral color and scent simultaneously. Taking these results together, the present study provides a preliminary deciphering of the genetic constraints underlying flower color and scent development, and proposes possible schemes for further genetic modification of ornamental traits in C. miniata and other plants.
Day Versus Night Melatonin and Corticosterone Modulation by LPS in Distinct Tissues of Toads (Rhinella Icterica)
Authors: Cyrino João Cunha , de Figueiredo Aymam Cobo , Córdoba-Moreno Marlina Olyissa , Gomes Fernando Ribeiro , Titon Stefanny Christie Monteiro 
Published: May 2022

Synopsis
Pathogen-associated molecular patterns modulate melatonin (MEL) production in the pineal and extra-pineal sites and corticosterone (CORT) synthesis in the adrenal/interrenal and other tissues. Both MEL and CORT play essential and complex immunomodulatory roles, controlling the inflammatory response. Given that most of what we know about these interactions is derived from mammalian studies, discovering how MEL and CORT are modulated following an immune challenge in anurans would increase understanding of how conserved these immune-endocrine interactions are in vertebrates. Herein, we investigated the modulation of MEL and CORT in plasma vs. local tissues of toads (Rhinella icterica) in response to an immune challenge with lipopolysaccharide (LPS; 2 mg/kg) at day and night. Blood samples were taken 2 hours after injection (noon and midnight), and individuals were killed for tissue collection (bone marrow, lungs, liver, and intestine). MEL and CORT were determined in plasma and tissue homogenates. LPS treatment increased MEL concentration in bone marrow during the day. Intestine MEL levels were higher at night than during the day, particularly in LPS-injected toads. Bone marrow and lungs showed the highest MEL levels among tissues. Plasma MEL levels were not affected by either the treatment or the phase. Plasma CORT levels increased in LPS-treated individuals, with an accentuated increase at night. Otherwise, CORT concentration in the tissues was not affected by LPS exposure. Modulation of MEL levels in bone marrow suggests this tissue may participate in the toad's inflammatory response assembly. Moreover, MEL and CORT levels were different in tissues, pointing to an independent modulation of hormonal concentration. Our results suggest an important role of immune challenge in modulating MEL and CORT, bringing essential insights into the hormone-immune interactions during anuran's inflammatory response.
Comparison of algorithms for identifying people with HIV from electronic medical records in a large, multi-site database
Authors: Ridgway Jessica P , Mason Joseph A , Friedman Eleanor E , Devlin Samantha , Zhou Junlan , Meltzer David , Schneider John 
Published: May 2022

Abstract

Objective
As electronic medical record (EMR) data are increasingly used in HIV clinical and epidemiologic research, accurately identifying people with HIV (PWH) from EMR data is paramount. We sought to evaluate EMR data types and compare EMR algorithms for identifying PWH in a multicenter EMR database.

Materials and Methods
We collected EMR data from 7 healthcare systems in the Chicago Area Patient-Centered Outcomes Research Network (CAPriCORN) including diagnosis codes, anti-retroviral therapy (ART), and laboratory test results.

Results
In total, 13 935 patients had a positive laboratory test for HIV; 33 412 patients had a diagnosis code for HIV; and 17 725 patients were on ART. Only 8576 patients had evidence of HIV-positive status for all 3 data types (laboratory results, diagnosis code, and ART). A previously validated combination algorithm identified 22 411 patients as PWH.

Conclusion
EMR algorithms that combine laboratory results, administrative data, and ART can be applied to multicenter EMR data to identify PWH.
Effect of limestone solubility on mineral digestibility and bone ash in nursery pigs fed diets containing graded level of inorganic phosphorus or increasing dose of a novel consensus bacterial 6-phytase variant
Authors: Velayudhan Deepak E , Kumar Arun , Marchal Leon , Dersjant-Li Yuemig 
Published: May 2022

Abstract
The effect of a novel consensus bacterial 6-phytase variant (PhyG) on total tract digestibility (ATTD) of minerals and bone ash was evaluated in pigs fed diets containing medium- and high-solubility limestone (MSL and HSL, 69.6 and 91.7% solubility, respectively, at 5 min, pH 3.0) in a randomized complete block design. For each limestone, eight diets were formulated: an inorganic phosphate-free negative control (NC) based on wheat, corn, soybean-meal, canola-meal and rice-barn [0.18% standardized total tract digestible (STTD) P and 0.59% Ca]; the NC supplemented with 250, 500, 1,000, or 2,000 FTU/kg of PhyG, and; the NC with added monocalcium phosphate (MCP) and limestone to produce three positive controls (0.33, 0.27, and 0.21% STTD P, and 0.75, 0.70, and 0.64% Ca, respectively; PC1, PC2, PC3). In total, 128 pigs (12.8 ± 1.33 kg, 8 pigs/treatment, housed individually) were adapted for 16 d followed by 4 d of fecal collection. Femurs were collected from euthanized pigs on day 21. Data were analyzed by one-way ANOVA with means separation by Tukey’s test, and by factorial analysis (2 x 4: 2 levels of limestone solubility, 4 STTD P levels, and 2 × 5: 2 levels of limestone solubility, 5 PhyG dose levels). Phytase dose-response was analyzed by curve fitting. A consistent negative effect of HSL on ATTD P and Ca was observed in control diets (P &lt; 0.001). Across phytase-supplemented diets, HSL reduced (P &lt; 0.05) ATTD Ca and P (% and g/kg) compared with MSL. Across limestones, increasing phytase dose level increased (P &lt; 0.05) ATTD P exponentially. Limestone solubility had no effect on bone ash, but PhyG linearly increased (P &lt; 0.05) bone ash; 500 FTU/kg or higher maintained bone ash (g/femur) equivalent to PC1. In conclusion, ATTD P and Ca were reduced by a high compared with a medium soluble limestone, but the novel phytase improved ATTD P and Ca independent of limestone solubility.
Welding simulation using a reduced order model for efficient residual stress evaluation
Authors: Shin Han-Seop , Boo Seung-Hwan 
Published: May 2022

Abstract
In this paper, to evaluate the residual stress of welded structures efficiently, we propose a welding simulation method utilizing a reduced order model. To construct the reduced order model, a finite element model is divided into a target part and an omitted part. For the heat transfer analysis, a thermal boundary condition is newly defined and applied to the target part, to compensate for the heat loss induced by neglecting the omitted part. For the thermal elastic plastic analysis, a reduced model for the target part is constructed using the automated static condensation method. The performance of the proposed welding simulation method adopting the reduced order model is verified by solving several welding problems, and it effectively reduces computational costs while predicting the residual stress with little loss of accuracy.
On Risk and Time Pressure: When to Think and When to Do
Authors: Carnehl Christoph , Schneider Johannes 
Published: May 2022

AbstractWe study the tradeoff between fundamental risk and time. A time-constrained agent has to solve a problem. She dynamically allocates effort between implementing a risky initial idea and exploring alternatives. Discovering an alternative implies progress that has to be converted to a solution. As time runs out, the chances of converting it in time shrink. We show that the agent may return to the initial idea after having left it in the past to explore alternatives. Our model helps explain so-called false starts. To finish fast, the agent delays exploring alternatives, reducing the overall success probability.
Landscape Connectivity and Genetic Structure in a Mainstem and a Tributary Stonefly (Plecoptera) Species Using a Novel Reference Genome
Authors: Malison Rachel L , Hand Brian K , Winter Emily , Giersch J Joseph , Amish Stephen J , Whited Diane , Stanford Jack A , Luikart Gordon 
Published: May 2022

AbstractUnderstanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modeling to investigate how climatic and habitat variables relate to patterns of genetic variation in 2 stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO &gt; 95% using “insecta_ob9” reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis, but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.
A Vishnu-Come-Lately: John Bacon’s Monument to William Jones (1799)
Authors: Monks Sarah 
Published: May 2022

Abstract
This article considers John Bacon’s marble monument to one of eighteenth-century British colonialism’s most important protagonists, William Jones (1746–1794). A prodigious scholar of Indian languages, religions, and laws, as well as a Supreme Court judge in Bengal, Jones epitomized early orientalism, promoting the study of Indian cultures as a means of facilitating the East India Company’s ‘governmental’ regulation of colonial subjects in its own interests. However, by the time this monument was erected, that vision of British India was becoming a thing of the past, gradually replaced by a more self-consciously imperializing, Anglicizing approach. Reading the monument both with and against the grain, this article argues that the tensions inherent in the orientalist attitude towards India are registered within the monument itself, especially in the relationship between its statue of Jones and the Hindu imagery on its pedestal. For while that imagery pays tribute to Jones, especially through its iconographical depiction of Vishnu, the Hindu god of justice and protection, it is dominated by the undemonstrative yet emphatically present figure of an Indian woman, seemingly the monument’s sole visual reference to a colonized human subject. Existing somewhere between human and sculpture, and between human and divine, she resists meaning and knowledge, troubling the monument’s semantic clarity and commemorative purpose.
Cosmological evolution of gas and supermassive black holes in idealized isolated haloes
Authors: Dattathri Shashank , Sharma Prateek 
Published: May 2022

ABSTRACT
We study the evolution of baryonic gas in cosmologically growing dark matter haloes. To accurately model both the inner and outer regions of the haloes, we use a dark matter density profile that transitions smoothly from the Navarro–Frenk–White profile within the virial radius to a more realistic flat profile far beyond the halo. We construct a dark matter gravitational potential consistent with this density profile, and we use a ‘cosmological’ potential that accounts for gas evolution consistent with Hubble expansion at large radii. Gas is initialized with a density ≈ 0.2 times the dark matter density, consistent with the universal baryon fraction ρg/(ρg + ρDM) ≈ 0.17. We study the formation of the virial shock and evolution of the baryon fraction, including the effects of radiative cooling and active galactic nucleus jet feedback. The feedback is powered by the accretion of cold gas on to a central supermassive black hole (SMBH). The cores of the halo exhibit heating and cooling cycles, whose strength and duration depend on the feedback efficiency and the halo mass. The central SMBH initially grows exponentially with time in the early quasar phase, but the growth slows down at later times. The baryon fraction in the core decreases with increasing feedback efficiency and decreasing halo mass. While the halo outskirts evolve self-similarly, the core density is non-evolving, in agreement with cluster observations. We analyse the correlations between the properties of the gas and the central SMBH, and explore the existence of a Fundamental Plane.
Discovery of a highly eccentric, chromospherically active binary: ASASSN-V J192114.84+624950.8
Authors: Way Zachary S , Jayasinghe T , Kochanek C S , Stanek K Z , Vallely Patrick , Thompson Todd A , Holoien Thomas W-S , Shappee Benjamin J 
Published: May 2022

ABSTRACT
As part of an All-Sky Automated Survey for SuperNovae (ASAS-SN) search for sources with large flux decrements, we discovered a transient where the quiescent, stellar source ASASSN-V J192114.84+624950.8 rapidly decreased in flux by $\sim 55{{\ \rm per\ cent}}$ (∼0.9 mag) in the g band. The Transiting Exoplanet Survey Satellite light curve revealed that the source is a highly eccentric, eclipsing binary. Fits to the light curve using phoebe find the binary orbit to have e = 0.79, Porb = 18.462 d, and i = 88.6°, and the ratios of the stellar radii and temperatures to be R2/R1 = 0.71 and Te,2/Te,1 = 0.82. Both stars are chromospherically active, allowing us to determine their rotational periods of P1 = 1.52 d and P2 = 1.79 d, respectively. A Large Binocular Telescope/Multi-Object Double Spectrograph spectrum shows that the primary is a late-G- or early-K-type dwarf. Fits to the spectral energy distribution show that the luminosities and temperatures of the two stars are L1 = 0.48 L⊙, $T_1= 5050\, \mathrm{K}$, L2 = 0.12 L⊙, and $T_{2} = 4190\, \mathrm{K}$. We conclude that ASASSN-V J192114.84+624950.8 consists of two chromospherically active, rotational variable stars in a highly elliptical eclipsing orbit.
Detectability of a spatial correlation between stellar mass black hole mergers and active galactic nuclei in the local Universe
Authors: Veronesi Niccolò , Rossi Elena Maria , van Velzen Sjoert , Buscicchio Riccardo 
Published: May 2022

ABSTRACT
The origin of the binary black hole (BBH) mergers detected through gravitational waves (GWs) by the LIGO-Virgo-KAGRA (LVK) collaboration remains debated. One fundamental reason is our ignorance of their host environment, as the typical size of an event’s localization volume can easily contain thousands of galaxies. A strategy around this is to exploit statistical approaches to assess the spatial correlation between these mergers and astrophysically motivated host galaxy types, such as active galactic nuclei (AGNs). We use a likelihood ratio method to infer the degree of GW–AGN connection out to z = 0.2. We simulate BBH mergers whose components’ masses are sampled from a realistic distribution of the underlying population of black holes (BHs). Localization volumes for these events are calculated assuming two different interferometric network configurations. These correspond to the configuration of the third (O3) and of the upcoming fourth (O4) LVK observing runs. We conclude that the 13 BBH mergers detected during the third observing run at z ≤ 0.2 are not enough to reject with a 3σ significance the hypothesis according to which there is no connection between GW and AGNs more luminous than $\approx 10^{44.3}\rm {erg}\ \rm {s}^{-1}$, that have number density higher than 10−4.75 Mpc−3. However, 13 detections are enough to reject this no-connection hypothesis when rarer categories of AGNs are considered, with bolometric luminosities greater than $\approx 10^{45.5}\rm {erg}\ \rm {s}^{-1}$. We estimate that O4 results will potentially allow us to test fractional contributions to the total BBH merger population from AGNs of any luminosity higher than $80{{\ \rm per\ cent}}$.
New, Useful Criteria for Assessing the Evidence of Infection in Sepsis Research
Authors: Mellhammar Lisa , Elén Sixten , Ehrhard Simone , Bouma Hjalmar , Ninck Lorenz , Muntjewerff Eva , Wünsch Daniel , Bloos Frank , Malmström Erik , Linder Adam 
Published: May 2022

OBJECTIVES:
The Sepsis-3 definition states the clinical criteria for sepsis but lacks clear definitions of the underlying infection. To address the lack of applicable definitions of infection for sepsis research, we propose new criteria, termed the Linder-Mellhammar criteria of infection (LMCI). The aim of this study was to validate these new infection criteria.

DESIGN:
A multicenter cohort study of patients with suspected infection who were admitted to emergency departments or ICUs. Data were collected from medical records and from study investigators.

SETTING:
Four academic hospitals in Sweden, Switzerland, the Netherlands, and Germany.

PATIENTS:
A total of 934 adult patients with suspected infection or suspected sepsis.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Agreement of infection site classification was measured using the LMCI with Cohen κ coefficient, compared with the Calandra and Cohen definitions of infection and diagnosis on hospital discharge as references. In one of the cohorts, comparisons were also made to adjudications by an expert panel. A subset of patients was assessed for interobserver agreement.

MEASUREMENTS AND MAIN RESULTS:
The precision of the LMCI varied according to the applied reference. LMCI performed better than the Calandra and Cohen definitions (κ = 0.62 [95% CI, 0.59–0.65] vs κ = 0.43 [95% CI, 0.39–0.47], respectively) and the diagnosis on hospital discharge (κ = 0.57 [95% CI, 0.53–0.61] vs κ = 0.43 [95% CI, 0.39–0.47], respectively). The interobserver agreement for the LMCI was evaluated in 91 patients, with agreement in 77%, κ = 0.72 (95% CI, 0.60–0.85). When tested with adjudication as the gold standard, the LMCI still outperformed the Calandra and Cohen definitions (κ = 0.65 [95% CI, 0.60–0.70] vs κ = 0.29 [95% CI, 0.24–0.33], respectively).

CONCLUSIONS:
The LMCI is useful criterion of infection that is intended for sepsis research, in and outside of the ICU. Useful criteria for infection have the potential to facilitate more comparable sepsis research and exclude sepsis mimics from clinical studies, thus improving and simplifying sepsis research.