bluuebunny/crossref_metadata_2025_split huggingface dataset:
Root system size and root hair length are key phenes for nitrate acquisition and biomass production across natural variation in Arabidopsis
Authors: De Pessemier Jérôme , Moturu Taraka Ramji , Nacry Philippe , Ebert Rebecca , De Gernier Hugues , Tillard Pascal , Swarup Kamal , Wells Darren M , Haseloff Jim , Murray Seth C , Bennett Malcolm J , Inzé Dirk , Vincent Christopher I , Hermans Christian 
Published: March 2022

Abstract
The role of root phenes in nitrogen (N) acquisition and biomass production was evaluated in 10 contrasting natural accessions of Arabidopsis thaliana L. Seedlings were grown on vertical agar plates with two different nitrate supplies. The low N treatment increased the root to shoot biomass ratio and promoted the proliferation of lateral roots and root hairs. The cost of a larger root system did not impact shoot biomass. Greater biomass production could be achieved through increased root length or through specific root hair characteristics. A greater number of root hairs may provide a low-resistance pathway under elevated N conditions, while root hair length may enhance root zone exploration under low N conditions. The variability of N uptake and the expression levels of genes encoding nitrate transporters were measured. A positive correlation was found between root system size and high-affinity nitrate uptake, emphasizing the benefits of an exploratory root organ in N acquisition. The expression levels of NRT1.2/NPF4.6, NRT2.2, and NRT1.5/NPF7.3 negatively correlated with some root morphological traits. Such basic knowledge in Arabidopsis demonstrates the importance of root phenes to improve N acquisition and paves the way to design eudicot ideotypes.
3D models of the circumstellar environments of evolved stars: Formation of multiple spiral structures
Authors: Aydi Elias , Mohamed Shazrene 
Published: March 2022

ABSTRACTWe present 3D hydrodynamic models of the interaction between the outflows of evolved, pulsating, Asymptotic Giant Branch (AGB) stars and nearby (&lt;3 stellar radii) substellar companions (Mcomp ≲ 40 MJ). Our models show that due to resonances between the orbital period of the companion and the pulsation period of the AGB star, multiple spiral structures can form; the shocks driven by the pulsations are enhanced periodically in different regions as they encounter the denser material created by the substellar companion’s wake. We discuss the properties of these spiral structures and the effect of the companion parameters on them. We also demonstrate that the gravitational potential of the nearby companion enhances the mass-loss from the AGB star. For more massive (Mcomp &gt; 40 MJ) and more distant companions (&gt;4 stellar radii), a single spiral arm forms. We discuss the possibility of observing these structures with the new generations of high-resolution, high-sensitivity instruments, and using them to ‘find’ substellar companions around bright, evolved stars. Our results also highlight possible structures that could form in our Solar system when the Sun turns into an AGB star.
Comparing the frequentist and Bayesian periodic signal detection: rates of statistical mistakes and sensitivity to priors
Authors: Baluev Roman V 
Published: March 2022

ABSTRACT
We perform extensive Monte Carlo simulations to systematically compare the frequentist and Bayesian treatments of the Lomb–Scargle periodogram. The goal is to investigate whether the Bayesian period search is advantageous over the frequentist one in terms of the detection efficiency, how much if yes, and how sensitive it is regarding the choice of the priors, in particular in case of a misspecified prior (whenever the adopted prior does not match the actual distribution of physical objects). We find that the Bayesian and frequentist analyses always offer nearly identical detection efficiency in terms of their trade-off between type-I and type-II mistakes. Bayesian detection may reveal a formal advantage if the frequency prior is non-uniform, but this results in only ∼1 per cent extra detected signals. In case if the prior was misspecified (adopting non-uniform one over the actual uniform) this may turn into an opposite advantage of the frequentist analysis. Finally, we revealed that Bayes factor of this task appears rather overconservative if used without a calibration against type-I mistakes (false positives), thereby necessitating such a calibration in practice.
Gas-phase metallicity determinations in nearby AGNs with SDSS-IV MaNGA: evidence of metal-poor accretion
Authors: do Nascimento Janaína C , Dors Oli L , Storchi-Bergmann Thaisa , Mallmann Nícolas D , Riffel Rogério , Ilha Gabriele S , Riffel Rogemar A , Rembold Sandro B , Deconto-Machado Alice , da Costa Luiz N , Armah Mark 
Published: March 2022

ABSTRACTWe derive the metallicity (traced by the O/H abundance) of the narrow-line region (NLR) of 108 Seyfert galaxies as well as radial metallicity gradients along their galaxy discs and of these of a matched control sample of no active galaxies. In view of that, observational data from the SDSS-IV MaNGA survey and strong emission-line calibrations taken from the literature were considered. The metallicity obtained for the NLRs was compared to the value derived from the extrapolation of the radial oxygen abundance gradient, obtained from H ii region estimates along the galaxy disc, to the central part of the host galaxies. We find that, for most of the objects ($\sim 80\, {{\ \rm per\ cent}}$), the NLR metallicity is lower than the extrapolated value, with the average difference ($\langle$D$\rangle$) between these estimates ranging from 0.16 to 0.30 dex. We suggest that $\langle$D$\rangle$ is due to the accretion of metal-poor gas to the AGN that feeds the nuclear supermassive black hole (SMBH), which is drawn from a reservoir molecular and/or neutral hydrogen around the SMBH. Additionally, we look for correlations between D and the electron density (Ne), [O iii]λ5007, and H α luminosities, extinction coefficient (AV) of the NLRs, as well as the stellar mass (M*) of the host galaxies. Evidence of an inverse correlation between the D and the parameters Ne, M*, and Av was found.
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function
Authors: Martin Darren P. , Lytras Spyros , Lucaci Alexander G. , Maier Wolfgang , Grüning Björn , Shank Stephen D. , Weaver Steven , MacLean Oscar A. , Orton Richard J. , Lemey Philippe , Boni Maciej F. , Tegally Houriiyah , Harkins Gordon W. , Scheepers Cathrine , Bhiman Jinal N. , Everatt Josie , Amoako Daniel G. , San James Emmanuel , Giandhari Jennifer , Sigal Alex , Williamson Carolyn , Hsiao Nei-yuan , von Gottberg Anne , De Klerk Arne , Shafer Robert W. , Robertson David L. , Wilkinson Robert J. , Sewell B. Trevor , Lessells Richard , Nekrutenko Anton , Greaney Allison J. , Starr Tyler N. , Bloom Jesse D. , Murrell Ben , Wilkinson Eduan , Gupta Ravindra K. , de Oliveira Tulio , Kosakovsky Pond Sergei L. 
Published: March 2022

Abstract
Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (1) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (2) interactions of Spike with ACE2 receptors, and (3) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron overall previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.
Vitamin D concentrations during pregnancy and in cord blood: a systematic review and meta-analysis
Authors: Wong Rosa S , Tung Keith T S , Mak Ray T W , Leung Wing Cheong , Yam Jason C , Chua Gilbert T , Fung Genevieve P G , Ho Macro H K , Wong Ian C K , Ip Patrick 
Published: March 2022

Abstract

Context
Effect size estimates for the association between vitamin D concentrations in maternal blood during pregnancy and in cord blood vary widely across studies, but no meta-analysis has been conducted to ascertain this association.

Objective
The aim of this systematic review was to estimate the pooled effect size for the association between circulating 25-hydroxyvitamin D (25[OH]D) concentrations, a marker of vitamin D status, in maternal blood during pregnancy and in cord blood.

Data Sources
The PubMed, Embase, and Web of Science databases were searched from their inception to February 2021.

Data Extraction
Following the application of prespecified inclusion and exclusion criteria, 94 articles were eligible for full-text review, which was conducted by 2 authors independently. A third author was consulted when necessary and consensus reached. In total, 26 articles, which comprised 30 studies and 6212 mother-infant dyads, were included. Methodological quality was assessed using a modified version of the Joanna Briggs Institute’s Critical Appraisal Checklist for Studies Reporting Prevalence Data. Correlation coefficient (r) values for the association between maternal serum 25(OH)D concentrations during pregnancy and in cord blood were extracted.

Data Analysis
The r values were pooled using random-effects meta-analyses. Sensitivity and subgroup analyses were performed to investigate sources of heterogeneity. The pooled r for all studies was 0.72 (95%CI, 0.64–0.79), indicating high heterogeneity (I2 = 95%, P &lt; 0.01). After influential and outlier studies were removed, the pooled r for 9 studies was 0.70 (95%CI, 0.66–0.74), which resulted in a substantial reduction in heterogeneity (I2 = 41%, P=0.10).

Conclusion
The findings support a positive and large correlation between maternal vitamin D concentrations during pregnancy and vitamin D concentrations in cord blood.

Systematic Review Registration
PROSPERO registration number CRD42021273348.
Suzaku observations of Fe K-shell lines in the supernova remnant W 51 C and hard X-ray sources in the proximity
Authors: Shimaguchi Aika , Nobukawa Kumiko K , Yamauchi Shigeo , Nobukawa Masayoshi , Fujita Yutaka 
Published: March 2022

Abstract
In this paper, we investigate the Fe K-shell lines in the supernova remnant W 51 C and hard X-ray sources in the proximity. We measure the intensities of the Fe i Kα and Fe xxv Heα lines at 6.40 and 6.68 keV, respectively, and find that the intensity of the 6.68 keV line is consistent with the background level expected from previous studies, while that of the 6.40 keV line is higher at the significance level of 2.0σ. Given the presence of gamma-ray emission and high ionization rate point spatially coincident with the remnant, we conclude that the enhanced 6.40 keV line most likely originates from the interaction between low-energy cosmic rays and molecular clouds. Also, we discover an enhanced 6.68 keV line emission from the compact H ii region G49.0−0.3 at a significance level of 3.4σ. Spectral analysis reveals that the temperature and abundance of the thermal plasma with the 6.68 keV line is $kT=3.0^{+0.8}_{-0.7}$ keV and Z = 0.5 ± 0.2 solar, respectively. These values are explained by the thermal plasma generated by the stellar winds of O stars.
Trimeric photosystem I facilitates energy transfer from phycobilisomes in Synechocystis sp. PCC 6803
Authors: Akhtar Parveen , Biswas Avratanu , Balog-Vig Fanny , Domonkos Ildikó , Kovács László , Lambrev Petar H 
Published: March 2022

Abstract
In cyanobacteria, phycobilisomes (PBS) serve as peripheral light-harvesting complexes of the two photosystems, extending their antenna size and the wavelength range of photons available for photosynthesis. The abundance of PBS, the number of phycobiliproteins they contain, and their light-harvesting function are dynamically adjusted in response to the physiological conditions. PBS are also thought to be involved in state transitions that maintain the excitation balance between the two photosystems. Unlike its eukaryotic counterpart, PSI is trimeric in many cyanobacterial species and the physiological significance of this is not well understood. Here, we compared the composition and light-harvesting function of PBS in cells of Synechocystis sp. PCC 6803, which has primarily trimeric PSI, and the ΔpsaL mutant, which lacks the PsaL subunit of PSI and is unable to form trimers. We also investigated a mutant additionally lacking the PsaJ and PsaF subunits of PSI. Both strains with monomeric PSI accumulated significantly more allophycocyanin per chlorophyll, indicating higher abundance of PBS. On the other hand, a higher phycocyanin:allophycocyanin ratio in the wild type suggests larger PBS or the presence of APC-less PBS (CpcL-type) that are not assembled in cells with monomeric PSI. Steady-state and time-resolved fluorescence spectroscopy at room temperature and 77 K revealed that PSII receives more energy from the PBS at the expense of PSI in cells with monomeric PSI, regardless of the presence of PsaF. Taken together, these results show that the oligomeric state of PSI impacts the excitation energy flow in Synechocystis.
MAP KINASE PHOSPHATASE1 promotes osmotolerance by suppressing PHYTOALEXIN DEFICIENT4-independent immunity
Authors: Uchida Kohei , Yamaguchi Masahiro , Kanamori Kazuki , Ariga Hirotaka , Isono Kazuho , Kajino Takuma , Tanaka Keisuke , Saijo Yusuke , Yotsui Izumi , Sakata Yoichi , Taji Teruaki 
Published: March 2022

Abstract
Initial exposure of plants to osmotic stress caused by drought, cold, or salinity leads to acclimation, termed acquired tolerance, to subsequent severe stresses. Acquired osmotolerance induced by salt stress is widespread across Arabidopsis (Arabidopsis thaliana) accessions and is conferred by disruption of a nucleotide-binding leucine-rich repeat gene, designated ACQUIRED OSMOTOLERANCE. De-repression of this gene under osmotic stress causes detrimental autoimmunity via ENHANCED DISEASE SUSCEPTIBILITY1 and PHYTOALEXIN DEFICIENT4 (PAD4). However, the mechanism underlying acquired osmotolerance remains poorly understood. Here, we isolated an acquired osmotolerance-defective mutant (aod13) by screening 30,000 seedlings of an ion beam-mutagenized M2 population of Bu-5, an accession with acquired osmotolerance. We found that AOD13 encodes the dual-specificity phosphatase MAP KINASE PHOSPHATASE1 (MKP1), which negatively regulates MITOGEN-ACTIVATED PROTEIN KINASE3/6 (MPK3/6). Consistently, MPK3/6 activation was greater in aod13 than in the Bu-5 wild-type (WT). The aod13 mutant was sensitive to osmotic stress but tolerant to salt stress. Under osmotic stress, pathogenesis-related genes were strongly induced in aod13 but not in the Bu-5 WT. Loss of PAD4 in pad4 aod13 plants did not restore acquired osmotolerance, implying that activation of immunity independent of PAD4 renders aod13 sensitive to osmotic stress. These findings suggest that AOD13 (i.e. MKP1) promotes osmotolerance by suppressing the PAD4-independent immune response activated by MPK3/6.
Primary Care Physical Therapists’ Experiences When Screening for Serious Pathologies Among Their Patients: A Qualitative Study
Authors: Budtz Cecilie Rud , Rønn-Smidt Helle , Thomsen Janus Nikolaj Laust , Hansen Rikke Pilegaard , Christiansen David Høyrup 
Published: March 2022

Abstract

Objective
A vital part of the initial examination performed by a physical therapist is to establish whether the patient would benefit from physical therapist intervention. This process includes knowledge about contraindications for treatment and screening for serious pathologies. However, little is known about the physical therapists' views and thoughts about their own practice when screening for serious pathologies. The purpose of this study was to explore the experience gained by physical therapists when screening for serious pathologies among their patients.

Methods
This was a qualitative study based on individual semi-structured interviews with 9 primary care physical therapists. The interviews were analyzed using reflexive thematic analysis, and generated themes were explained and reported with relevant quotes.

Results
Three overall themes were generated: (1) the role of physical therapists in the diagnostic process; (2) responsibility from the individual to the group; and (3) the difficult task of cooperation. The physical therapists described how they relied more on their clinical suspicion than on asking red-flag questions when screening for serious pathologies. They also questioned their differential diagnostic abilities. Finally, they saw a potential to further enhance their confidence in the area by reflecting on the matter with colleagues and by receiving more feedback about their clinical reasoning regarding serious pathologies from general practitioners.

Conclusion
These findings suggest that physical therapists primarily rely on their clinical suspicion when screening for serious pathologies but at the same time are uncertain about their differential diagnostic abilities.

Impact
These findings can inform future interventions targeting the physical therapists' abilities to detect serious pathology.
Using patient-reported data from a smartphone app to capture and characterize real-time patient-reported flares in rheumatoid arthritis
Authors: Gandrup Julie , Selby David A , van der Veer Sabine N , Mcbeth John , Dixon William G 
Published: March 2022

Abstract

Objective
We aimed to explore the frequency of self-reported flares and their association with preceding symptoms collected through a smartphone app by people with RA.

Methods
We used data from the Remote Monitoring of RA study, in which patients tracked their daily symptoms and weekly flares on an app. We summarized the number of self-reported flare weeks. For each week preceding a flare question, we calculated three summary features for daily symptoms: mean, variability and slope. Mixed effects logistic regression models quantified associations between flare weeks and symptom summary features. Pain was used as an example symptom for multivariate modelling.

Results
Twenty patients tracked their symptoms for a median of 81 days (interquartile range 80, 82). Fifteen of 20 participants reported at least one flare week, adding up to 54 flare weeks out of 198 participant weeks in total. Univariate mixed effects models showed that higher mean and steeper upward slopes in symptom scores in the week preceding the flare increased the likelihood of flare occurrence, but the association with variability was less strong. Multivariate modelling showed that for pain, mean scores and variability were associated with higher odds of flare, with odds ratios 1.83 (95% CI, 1.15, 2.97) and 3.12 (95% CI, 1.07, 9.13), respectively.

Conclusion
Our study suggests that patient-reported flares are common and are associated with higher daily RA symptom scores in the preceding week. Enabling patients to collect daily symptom data on their smartphones might, ultimately, facilitate prediction and more timely management of imminent flares.
DOSIMETRY IN DIGITAL BREAST TOMOSYNTHESIS: COST-EFFICIENT APPROACH FOR THE SOUTH AMERICAN PERSPECTIVES
Authors: Pirchio Rosana , Pérez Gonzalo Nicolás , Ratto Santiago Scinardo , Stefanic Amalia María 
Published: March 2022

Abstract
The measurement of air kerma in air (Kair) to estimate average glandular dose (AGD) received during digital breast tomosynthesis (DBT) studies is sometimes a difficult task. In this work, a novel methodology was implemented to measure Kair and half-value layer while the X-ray tube is rotating. A low economic cost support (LCS) was built to place aluminium sheets and a calibrated dosemeter. Three Fujifilm Innovality equipment were used and two dosemeters calibrated on W–Al energies. Validation of the new methodology was made against standard scheme and it was applied to estimate AGD for 300 patients and 7 phantoms. Validation analysis was satisfactory. The difference in the AGD calculated with the LCS and DICOM Header was lower than ±10%. AGD values ranged from 0.77 to 2.11 mGy and 0.85 to 2.15 mGy for phantoms and patients, respectively. The novel methodology has a potential use for DBT equipment without stationary mode.
Predicting stress and depressive symptoms using high-resolution smartphone data and sleep behavior in Danish adults
Authors: Otte Andersen Thea , Skovlund Dissing Agnete , Rosenbek Severinsen Elin , Kryger Jensen Andreas , Thanh Pham Vi , Varga Tibor V , Hulvej Rod Naja 
Published: March 2022

Abstract

Study Objectives
The early detection of mental disorders is crucial. Patterns of smartphone behavior have been suggested to predict mental disorders. The aim of this study was to develop and compare prediction models using a novel combination of smartphone and sleep behavior to predict early indicators of mental health problems, specifically high perceived stress and depressive symptoms.

Methods
The data material included two separate population samples nested within the SmartSleep Study. Prediction models were trained using information from 4522 Danish adults and tested in an independent test set comprising of 1885 adults. The prediction models utilized comprehensive information on subjective smartphone behavior, objective night-time smartphone behavior, and self-reported sleep behavior. Receiver operating characteristics area-under-the-curve (ROC AUC) values obtained in the test set were recorded as the performance metrics for each prediction model.

Results
Neither subjective nor objective smartphone behavior was found to add additional predictive information compared to basic sociodemographic factors when forecasting perceived stress or depressive symptoms. Instead, the best performance for predicting poor mental health was found in the sleep prediction model (AUC = 0.75, 95% CI: 0.72–0.78) for perceived stress and (AUC = 0.83, 95%CI: 0.80–0.85) for depressive symptoms, which included self-reported information on sleep quantity, sleep quality and the use of sleep medication.

Conclusions
Sleep behavior is an important predictor when forecasting mental health symptoms and it outperforms novel approaches using objective and subjective smartphone behavior.