bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host species shape the community structure of culturable endophytes in fruits of wild berry species (Vaccinium myrtillus L., Empetrum nigrum L. and Vaccinium vitis-idaea L.)
Authors: Nguyen Minh-Phuong , Lehosmaa Kaisa , Martz Françoise , Koskimäki Janne J , Pirttilä Anna Maria , Häggman Hely 
Published: July 2021

ABSTRACT
Wild berries are interesting research subjects due to their rich sources of health-beneficial phenolic compounds. However, the internal microbial communities, endophytes, associated with the wild berry fruits are currently unknown. Endophytes are bacteria or fungi inhabiting inside plant tissues, and their functions vary depending on the host species and environmental parameters. The present study aimed to examine community composition of fungal and bacterial endophytes in fruits of three wild berry species (bilberry Vaccinium myrtillus L., lingonberry Vaccinium vitis-idaea L. and crowberry Empetrum nigrum L.) and the effects of host plant species and their growth sites on shaping the endophytic communities. We found that the endophytic community structures differed between the berry species, and fungi were predominant over bacteria in the total endophytic taxa. We identified previously unknown endophytic fungal taxa including Angustimassarina, Dothidea, Fellozyma, Pseudohyphozyma, Hannaella coprosmae and Oberwinklerozyma straminea. A role of soluble phenolic compounds, the intracellular components in wild berry fruits, in shaping the endophytic communities is proposed. Overall, our study demonstrates that each berry species harbors a unique endophytic community of microbes.
Apt interpretation of comprehensive lipoprotein data in large-scale epidemiology: disclosure of fundamental structural and metabolic relationships
Authors: Ala-Korpela Mika , Zhao Siyu , Järvelin Marjo-Riitta , Mäkinen Ville-Petteri , Ohukainen Pauli 
Published: July 2021

Abstract

Background
Quantitative lipoprotein analytics using nuclear magnetic resonance (NMR) spectroscopy is currently commonplace in large-scale studies. One methodology has become widespread and is currently being utilized also in large biobanks. It allows the comprehensive characterization of 14 lipoprotein subclasses, clinical lipids, apolipoprotein A-I and B. The details of these data are conceptualized here in relation to lipoprotein metabolism with particular attention on the fundamental characteristics of subclass particle numbers, lipid concentrations and compositional measures.

Methods and Results
The NMR methodology was applied to fasting serum samples from Northern Finland Birth Cohorts 1966 and 1986 with 5651 and 5605 participants, respectively. All results were highly consistent between the cohorts. Circulating lipid concentrations in a particular lipoprotein subclass arise predominantly as the result of the circulating number of those subclass particles. The spherical lipoprotein particle shape, with a radially oriented surface monolayer, imposes size-dependent biophysical constraints for the lipid composition of individual subclass particles and inherently restricts the accommodation of metabolic changes via compositional modifications. The new finding that the relationship between lipoprotein subclass particle concentrations and the particle size is log-linear reveals that circulating lipoprotein particles are also under rather strict metabolic constraints for both their absolute and relative concentrations.

Conclusions
The fundamental structural and metabolic relationships between lipoprotein subclasses elucidated in this study empower detailed interpretation of lipoprotein metabolism. Understanding the intricate details of these extensive data is important for the precise interpretation of novel therapeutic opportunities and for fully utilizing the potential of forthcoming analyses of genetic and metabolic data in large biobanks.
Estimated Prevalence and Number of Persons With Isolated Antibody to Hepatitis B Core Antigen and Associated Occult Hepatitis B, United States, 2001–2018
Authors: Spradling Philip R , Xing Jian , Harris Aaron M , Ly Kathleen N 
Published: July 2021

Abstract
Persons with isolated antibody to hepatits B virus (HBV) core antigen (IAHBc) may have occult HBV infection (OBI), which is associated with reactivation and potential risk for hepatocellular carcinoma and HBV transmission. We used National Health and Nutrition Examination Survey data to estimate US IAHBc prevalence and published studies of IAHBc-associated OBI prevalence to estimate OBI burden. During 2001−2018, the prevalence of IAHBc was 0.8% (approximately 2.1 million persons), and the OBI burden range was 35 500–83 600 persons. These data support the need for more robust estimates of IAHBc-associated OBI prevalence in the general US population.
Scaling and Structural Properties of Juvenile Bull Kelp (Nereocystis luetkeana)
Authors: Dobkowski Katie A , Crofts Stephanie B 
Published: July 2021

Synopsis
Bull kelp (Nereocystis luetkeana), the only canopy-forming kelp in the Salish Sea, provides primary production in the nearshore subtidal environment and serves as an important habitat for economically and ecologically important species. An annual species, each year juvenile bull kelp sporophytes must grow from the hydrodynamically more benign benthos to the water column, where they experience substantial drag at the surface. Because of the differences in morphology and ecology across life stages, and the fact that previous work has focused mainly on adult bull kelp, we tested whether morphology and structural properties change with stipe length, investigating scaling of both juvenile (stipe length &lt; 40 cm) and mature (stipe length &gt; 40 cm) kelp, and testing how juvenile stipes fail. Juvenile bull kelp grow proportionally (isometric growth) when young, but lengthen more quickly than would be predicted by bulb size (negative allometry) at maturity. Based on our data, the predicted breakpoint between isometric and allometric growth occurred at about 33 cm, likely approximately one to two weeks of growth. Cross-sectional area of the stipe, force to failure, work to failure, and stiffness (Young's modulus) all grow more slowly than would be predicted based on length, while maximum stress and toughness increase more quickly than predicted. There is no change in extensibility over the size range we tested, suggesting that this material property does not change with stipe length. The differences in biomechanics between juvenile and adult kelp are likely a response to the varied hydrodynamic environments experienced during the annual life cycle, which highlights the importance of studying organisms across life stages.
Overcoming gaps: regional collaborative to optimize capacity management and predict length of stay of patients admitted with COVID-19
Authors: Usher Michael G , Tourani Roshan , Simon Gyorgy , Tignanelli Christopher , Jarabek Bryan , Strauss Craig E , Waring Stephen C , Klyn Niall A M , Kealey Burke T , Tambyraja Rabindra , Pandita Deepti , Baum Karyn D 
Published: July 2021

Abstract

Objective
Ensuring an efficient response to COVID-19 requires a degree of inter-system coordination and capacity management coupled with an accurate assessment of hospital utilization including length of stay (LOS). We aimed to establish optimal practices in inter-system data sharing and LOS modeling to support patient care and regional hospital operations.

Materials and Methods
We completed a retrospective observational study of patients admitted with COVID-19 followed by 12-week prospective validation, involving 36 hospitals covering the upper Midwest. We developed a method for sharing de-identified patient data across systems for analysis. From this, we compared 3 approaches, generalized linear model (GLM) and random forest (RF), and aggregated system level averages to identify features associated with LOS. We compared model performance by area under the ROC curve (AUROC).

Results
A total of 2068 patients were included and used for model derivation and 597 patients for validation. LOS overall had a median of 5.0 days and mean of 8.2 days. Consistent predictors of LOS included age, critical illness, oxygen requirement, weight loss, and nursing home admission. In the validation cohort, the RF model (AUROC 0.890) and GLM model (AUROC 0.864) achieved good to excellent prediction of LOS, but only marginally better than system averages in practice.

Conclusion
Regional sharing of patient data allowed for effective prediction of LOS across systems; however, this only provided marginal improvement over hospital averages at the aggregate level. A federated approach of sharing aggregated system capacity and average LOS will likely allow for effective capacity management at the regional level.
PCYT2 synthesizes CDP-glycerol in mammals and reduced PCYT2 enhances the expression of functionally glycosylated α-dystroglycan
Authors: Imae Rieko , Manya Hiroshi , Tsumoto Hiroki , Miura Yuri , Endo Tamao 
Published: July 2021

Abstract
α-Dystroglycan (α-DG) is a highly glycosylated cell-surface protein. Defective O-mannosyl glycan on α-DG is associated with muscular dystrophies and cancer. In the biosynthetic pathway of the O-mannosyl glycan, fukutin (FKTN) and fukutin-related protein (FKRP) transfer ribitol phosphate (RboP). Previously, we reported that FKTN and FKRP can also transfer glycerol phosphate (GroP) from CDP-glycerol (CDP-Gro) and showed the inhibitory effects of CDP-Gro on functional glycan synthesis by preventing glycan elongation in vitro. However, whether mammalian cells have CDP-Gro or associated synthetic machinery has not been elucidated. Therefore, the function of CDP-Gro in mammals is largely unknown. Here, we reveal that cultured human cells and mouse tissues contain CDP-Gro using liquid chromatography tandem–mass spectrometry (LC–MS/MS). By performing the enzyme activity assay of candidate recombinant proteins, we found that ethanolamine-phosphate cytidylyltransferase (PCYT2), the key enzyme in de novo phosphatidylethanolamine biosynthesis, has CDP-Gro synthetic activity from glycerol-3-phosphate (Gro3P) and CTP. In addition, knockdown of PCYT2 dramatically reduced cellular CDP-Gro. These results indicate that PCYT2 is a CDP-Gro synthase in mammals. Furthermore, we found that the expression of functionally glycosylated α-DG is increased by reducing PCYT2 expression. Our results suggest an important role for CDP-Gro in the regulation of α-DG function in mammals.
Improving C4 photosynthesis to increase productivity under optimal and suboptimal conditions
Authors: Sales Cristina R G , Wang Yu , Evers Jochem B , Kromdijk Johannes 
Published: July 2021

Abstract
Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area is strongly biased towards species with C3 photosynthesis relative to C4 species. Here, we outline potential strategies for improving C4 photosynthesis to increase yields in crops by reviewing the major bottlenecks limiting the C4 NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state C4 photosynthesis under non-stressed conditions can be enhanced by increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative bottlenecks for photosynthetic performance under drought, heat, or chilling stress or during photosynthetic induction await further experimental verification. Based on source–sink interactions in maize, sugarcane, and sorghum, alleviating these photosynthetic bottlenecks during establishment and growth of the harvestable parts are likely to improve yield. The expected benefits are also shown to be augmented by the increasing trend in planting density, which increases the impact of photosynthetic source limitation on crop yields.
Mapping the Galactic centre’s dark cluster via resonant relaxation
Authors: Tep Kerwann , Fouvry Jean-Baptiste , Pichon Christophe , Heißel Gernot , Paumard Thibaut , Perrin Guy , Vincent Frederic 
Published: July 2021

ABSTRACT
Supermassive black holes in the centre of galaxies dominate the gravitational potential of their surrounding stellar clusters. In these dense environments, stars follow nearly Keplerian orbits, which get slowly distorted as a result of the potential fluctuations generated by the stellar cluster itself. In particular, stars undergo a rapid relaxation of their eccentricities through both resonant and non-resonant processes. An efficient implementation of the resonant diffusion coefficients allows for detailed and systematic explorations of the parameter space describing the properties of the stellar cluster. In conjunction with recent observations of the S-cluster orbiting SgrA*, this framework can be used to jointly constrain the distribution of the unresolved, old, background stellar cluster and the characteristics of a putative dark cluster. Specifically, we show how this can be used to estimate the typical mass and cuspide exponent of intermediate-mass black holes consistent with the relaxed state of the distribution of eccentricities in the observed S-cluster. This should prove useful in constraining supermassive black hole formation scenarios.
Dissecting theGaiaHR diagram within 200 pc
Authors: Dal Tio Piero , Mazzi Alessandro , Girardi Léo , Barbieri Mauro , Zaggia Simone , Bressan Alessandro , Chen Yang , Costa Guglielmo , Marigo Paola 
Published: July 2021

ABSTRACTWe analyse the high-quality Hertzsprung–Russell diagram (HRD) derived from Gaia data release 2 for the Solar Neighbourhood. We start building an almost complete sample within 200 pc and for |b| &gt; 25○, so as to limit the impact of known errors and artefacts in the Gaia catalogue. Particular effort is then put into improving the modelling of population of binaries, which produce two marked features in the HRD: the sequence of near-equal mass binaries along the lower main sequence, and the isolated group of hot subdwarfs. We describe a new tool, BinaPSE, to follow the evolution of interacting binaries in a way that improves the consistency with PARSEC evolutionary tracks for single stars. BinaPSE is implemented into the TRILEGAL code for the generation of ‘partial models’ for both single and binary stellar populations, taking into account the presence of resolved and unresolved binaries. We then fit the Gaia HRD via Markov chain Monte Carlo methods that search for the star formation history and an initial binary fraction (by mass) that maximize the likelihood. The main results are (i) the binary fraction derived from the lower MS is close to 0.4, while twice larger values are favoured when the upper part of the HRD is fitted; (ii) present models predict the observed numbers of hot subdwarfs to within a factor of 2; and (iii) irrespective of the prescription for the binaries, the star formation rate peaks at values $\sim \!1.5\times 10^{-4}{\rm{M}_{\odot }}\mathrm{yr}^{-1}$ at ages slightly above 2 Gyr, and then decreases to $\sim \!0.8\times 10^{-4}{\rm{M}_{\odot }}\mathrm{yr}^{-1}$ at very old ages.
The frequency by mass of Galactic carbon stars inferred from Gaia measurements of star cluster members
Authors: Pal Tathagata , Worthey G 
Published: July 2021

ABSTRACT
We investigate the frequency of occurrence of Galactic carbon stars as a function of progenitor mass using Gaia data. Small number statistics limit fidelity, but C-star frequency agrees with that observed in the Magellanic Clouds (MCs) down to m ≈ 1.67 M⊙. At m ≈ 1.38 M⊙, the frequency rises by a factor of three even though the frequency appears to drop to zero for the MCs. In fact this is due to a lack of clusters at the key age range in the MCs. At m ≈ 1.24 M⊙ and below, no C-stars are observed, corresponding to ages older than 4 Gyr. Within uncertainties, C-star frequency in M 31 is consistent with that of the Galaxy and the MCs. We find an ambiguous C-star candidate at ∼7 M⊙.
HR-pypopstar: high-wavelength-resolution stellar populations evolutionary synthesis model
Authors: Millán-Irigoyen I , Mollá M , Cerviño M , Ascasibar Y , García-Vargas M L , Coelho P R T 
Published: July 2021

ABSTRACT
We present the HR-pyPopStar model, which provides a complete set (in ages) of high-resolution (HR) spectral energy distributions of Single Stellar Populations. The model uses the most recent high-wavelength-resolution theoretical atmosphere libraries for main-sequence, post-AGB/planetary nebulae and Wolf–Rayet stars. The spectral energy distributions are given for more than a hundred ages ranging from 0.1 Myr to 13.8 Gyr, at four different values of the metallicity (Z = 0.004, 0.008, 0.019, and 0.05), considering four different IMFs. The wavelength range goes from 91 to $24\, 000$ Å in linear steps δλ = 0.1 Å, giving a theoretical resolving power $R_{{\rm th},5000} \sim 50\, 000$ at 5000 Å. This is the main novelty of these spectra, unique for their age and wavelength ranges. The models include the ionizing stellar populations that are relevant at both young (massive hot stars) and old (planetary nebulae) ages. We have tested the results with some examples of HR spectra recently observed with MEGARA at GTC. We highlight the importance of wavelength resolution in reproducing and interpreting the observational data from the last and forthcoming generations of astronomical instruments operating at 8–10 m class telescopes, with higher spectral resolution than their predecessors.
The flare-activity of 2MASS J16111534–1757214 in the upper Scorpius association
Authors: Guenther E W , Wöckel D , Chaturvedi P , Kumar V , Srivastava M K , Muheki P 
Published: July 2021

ABSTRACT
Flares are known to play an important role for the evolution of the atmospheres of young planets. In order to understand the evolution of planets, it is thus important to study the flare-activity of young stars. This is particularly the case for young M-stars, because they are very active. We study photometrically and spectroscopically the highly active M-star 2MASS J16111534–1757214. We show that it is a member of the Upper Sco OB association, which has an age of 5–10 Myrs. We also re-evaluate the status of other bona-fide M-stars in this region and identify 42 members. Analyzing the K2-light curves, we find that 2MASS J16111534–1757214 has, on average, one super-flare with $\rm E\ge 10^{35}$ erg every 620 h, and one with $\rm E\ge 10^{34}$ erg every 52 h. Although this is the most active M-star in the Upper Sco association, the power-law index of its flare-distribution is similar to that of other M-stars in this region. 2MASS J16111534–1757214 as well as other M-stars in this region show a broken power-law distribution in the flare-frequency diagram. Flares larger than $\rm E \ge 3\, 10^{34}$ erg have a power-law index $\rm \beta =-1.3\pm 0.1$ and flares smaller than that $\rm \beta =-0.8\pm 0.1$. We furthermore conclude that the flare-energy distribution for young M-stars is not that different from solar-like stars.
Two extreme steep-spectrum, polarized radio sources towards the Galactic bulge
Authors: Hyman S D , Frail D A , Deneva J S , Kassim N E , Giacintucci S , Kooi J E , Lazio T J W , Joyner I , Peters W M , Gajjar V , Siemion A P V 
Published: July 2021

ABSTRACT
From an on-going survey of the Galactic bulge, we have discovered a number of compact, steep spectrum radio sources. In this study, we have carried out more detailed observations for two of these sources, located 43 arcmin and 12${_{.}^{\circ}}$7 from the Galactic Centre. Both sources have a very steep spectrum (α ≃ − 3) and are compact, with upper limits on the angular size of 1–2 arcsec. Their flux densities appear to be relatively steady on time-scales of years, months, and hours, with no indications of rapid variability or transient behaviour. We detect significant circularly polarized emission from both sources, but only weak or upper limits on linear polarization. Neither source has a counterpart at other wavelengths and deep, high-frequency searches fail to find pulsations. We compare their source properties with other known compact, non-thermal source populations in the bulge (e.g. X-ray binaries, magnetars, the Burper, and cataclysmic variables). Our existing data support the hypothesis that they are scatter broadened millisecond or recycled pulsars, either at the bulge or along the line of sight. We also consider the possibility that they may be a new population of Galactic radio sources which share similar properties as pulsars but lack pulsations; a hypothesis that can be tested by future large-scale synoptic surveys.
TSMiner: a novel framework for generating time-specific gene regulatory networks from time-series expression profiles
Authors: Han Mingfei , Liu Xian , Zhang Wen , Wang Mengnan , Bu Wenjing , Chang Cheng , Yu Miao , Li Yingxing , Tian Chunyan , Yang Xiaoming , Zhu Yunping , He Fuchu 
Published: July 2021

Abstract
Time-series gene expression profiles are the primary source of information on complicated biological processes; however, capturing dynamic regulatory events from such data is challenging. Herein, we present a novel analytic tool, time-series miner (TSMiner), that can construct time-specific regulatory networks from time-series expression profiles using two groups of genes: (i) genes encoding transcription factors (TFs) that are activated or repressed at a specific time and (ii) genes associated with biological pathways showing significant mutual interactions with these TFs. Compared with existing methods, TSMiner demonstrated superior sensitivity and accuracy. Additionally, the application of TSMiner to a time-course RNA-seq dataset associated with mouse liver regeneration (LR) identified 389 transcriptional activators and 49 transcriptional repressors that were either activated or repressed across the LR process. TSMiner also predicted 109 and 47 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways significantly interacting with the transcriptional activators and repressors, respectively. These findings revealed the temporal dynamics of multiple critical LR-related biological processes, including cell proliferation, metabolism and the immune response. The series of evaluations and experiments demonstrated that TSMiner provides highly reliable predictions and increases the understanding of rapidly accumulating time-series omics data.