bluuebunny/crossref_metadata_2025 huggingface dataset:
Age determination of galaxy merger remnant stars using asteroseismology
Authors: Borre Camilla C , Aguirre Børsen-Koch Víctor , Helmi Amina , Koppelman Helmer H , Nielsen Martin B , Rørsted Jakob L , Stello Dennis , Stokholm Amalie , Winther Mark L , Davies Guy R , Hon Marc , Kruijssen J M Diederik , Laporte Chervin F P , Reyes Claudia , Yu Jie
Published: June 2022

The Milky Way was shaped by the mergers with several galaxies in the past. We search for remnant stars that were born in these foreign galaxies and assess their ages in an effort to put upper limits on the merger times and thereby better understand the evolutionary history of our Galaxy. Using 5D-phase space information from Gaia eDR3, radial velocities from Gaia DR2 and chemical information from apogee DR16, we kinematically and chemically select 21 red giant stars belonging to former dwarf galaxies that merged with the Milky Way. With added asteroseismology from Kepler and K2 , we determine the ages of the 21 ex situ stars and 49 in situ stars with an average σage/age of ∼31 per cent. We find that all the ex situ stars are consistent with being older than 8 Gyr. While it is not possible to associate all the stars with a specific dwarf galaxy, we classify eight of them as Gaia-Enceladus/Sausage stars, which is one of the most massive mergers in our Galaxy’s history. We determine their mean age to be 9.5 ± 1.3 Gyr consistent with a merger time of 8–10 Gyr ago. The rest of the stars are possibly associated with Kraken, Thamnos, Sequoia, or another extragalactic progenitor. The age determination of ex situ stars paves the way to more accurately pinning down when the merger events occurred and hence provide tight constraints useful for simulating how these events unfolded.
The impact of gas disc flaring on rotation curve decomposition and revisiting baryonic and dark matter relations for nearby galaxies
Authors: Mancera Piña Pavel E , Fraternali Filippo , Oosterloo Tom , Adams Elizabeth A K , Teodoro Enrico di , Bacchini Cecilia , Iorio Giuliano
Published: June 2022

Gas discs of late-type galaxies are flared, with scale heights increasing with the distance from the galaxy centres and often reaching kpc scales. We study the effects of gas disc flaring on the recovered dark matter halo parameters from rotation curve decomposition. For this, we carefully select a sample of 32 dwarf and spiral galaxies with high-quality neutral gas, molecular gas, and stellar mass profiles, robust H i rotation curves obtained via 3D kinematic modelling, and reliable bulge-disc decomposition. By assuming vertical hydrostatic equilibrium, we derive the scale heights of the atomic and molecular gas discs and fit dark matter haloes to the rotation curves self-consistently. We find that the effect of the gas flaring in the rotation curve decomposition can play an important role only for the smallest, gas-dominated dwarfs, while for most of the galaxies, the effect is minor and can be ignored. We revisit the stellar- and baryon-to-halo mass relations (M*–M200 and Mbar–M200). Both relations increase smoothly up to $M_{200} \approx 10^{12}~\rm { M_\odot }$, with galaxies at this end having high M*/M200 and Mbar/M200 ratios approaching the cosmological baryon fraction. At higher M200, the relations show a larger scatter. Most haloes of our galaxy sample closely follow the concentration–mass (c200–M200) relation resulting from N-body cosmological simulations. Interestingly, the galaxies deviating above and below the relation have the highest and lowest stellar and baryon factions, respectively, which suggests that the departures from the c200–M200 law are regulated by adiabatic contraction and an increasing importance of feedback.
Diagnosing large-scale stellar magnetic fields using PCA on spectropolarimetric data
Authors: Lehmann L T , Donati J-F
Published: June 2022

Insights on stellar surface large-scale magnetic field topologies are usually drawn by applying Zeeman–Doppler Imaging (ZDI) to the observed spectropolarimetric time series. However, ZDI requires experience for reliable results to be reached and is based on a number of prior assumptions that may not be valid, e.g. when the magnetic topology is evolving on time-scales comparable to or shorter than the time span over which observations are collected. In this paper, we present a method based on Principal Component Analysis (PCA) applied to circularly polarized (Stokes V) line profiles of magnetic stars to retrieve the main characteristics of the parent large-scale magnetic topologies, like for instance, the relative strength of the poloidal and toroidal components, and the degree of axisymmetry of the dominant field component and its complexity (dipolar or more complex). We show that this method can also be used to diagnose the temporal variability of the large-scale magnetic field. Performing best for stars with moderate projected equatorial velocities hosting relatively simple magnetic field topologies, this new method is simpler than ZDI, making it convenient to rapidly diagnose the main characteristics of the large-scale fields of non-degenerate stars and to provide insights into the temporal evolution of the field topology.
A general framework to test gravity using galaxy clusters – VI. Realistic galaxy formation simulations to study clusters in modified gravity
Authors: Mitchell Myles A , Arnold Christian , Li Baojiu
Published: June 2022

We present a retuning of the IllustrisTNG baryonic physics model which can be used to run large-box realistic cosmological simulations with a lower resolution. This new model employs a lowered gas density threshold for star formation and reduced energy releases by stellar and black hole feedback. These changes ensure that our simulations can produce sufficient star formation to closely match the observed stellar and gas properties of galaxies and galaxy clusters, despite having ∼160 times lower mass resolution than the simulations used to tune the fiducial IllustrisTNG model. Using the retuned model, we have simulated Hu–Sawicki f(R) gravity within a 301.75 h−1 Mpc box. This is, to date, the largest simulation that incorporates both screened modified gravity and full baryonic physics, offering a large sample (∼500) of galaxy clusters and ∼8000 galaxy groups. We have reanalysed the effects of the f(R) fifth force on the scaling relations between the cluster mass and four observable proxies: the mass-weighted gas temperature, the Compton Y-parameter of the thermal Sunyaev–Zel’dovich effect, the X-ray analogue of the Y-parameter, and the X-ray luminosity. We show that a set of mappings between the f(R) scaling relations and their Lambda cold dark matter counterpart, which have been tested in a previous work using a much smaller cosmological volume, are accurate to within a few per cent for the Y-parameters and $\lesssim 7{{\ \rm per\ cent}}$ for the gas temperature for cluster-sized haloes ($10^{14}\, {\rm M}_{\odot }\lesssim M_{500}\lesssim 10^{15}\, {\rm M}_{\odot }$). These mappings will be important for unbiased constraints of gravity using the data from ongoing and upcoming cluster surveys.
Solar-to-supersolar sodium and oxygen absolute abundances for a ‘hot Saturn’ orbiting a metal-rich star
Authors: Nikolov Nikolay K , Sing David K , Spake Jessica J , Smalley Barry , Goyal Jayesh M , Mikal-Evans Thomas , Wakeford Hannah R , Rustamkulov Zafar , Deming Drake , Fortney Jonathan J , Carter Aarynn , Gibson Neale P , Mayne Nathan J
Published: June 2022

We present new analysis of infrared transmission spectroscopy of the cloud-free hot-Saturn WASP-96b performed with the Hubble and Spitzer Space Telescopes (HST and Spitzer). The WASP-96b spectrum exhibits the absorption feature from water in excellent agreement with synthetic spectra computed assuming a cloud-free atmosphere. The HST-Spitzer spectrum is coupled with Very Large Telescope (VLT) optical transmission spectroscopy which reveals the full pressure-broadened profile of the sodium absorption feature and enables the derivation of absolute abundances. We confirm and correct for a spectral offset of $\Delta R_{{\rm p}}/R_{\ast }=(-4.29^{+0.31}_{-0.37})\, \times 10^{-3}$ of the VLT data relative to the HST-Spitzer spectrum. This offset can be explained by the assumed radius for the common-mode correction of the VLT spectra, which is a well-known feature of ground-based transmission spectroscopy. We find evidence for a lack of chromospheric and photometric activity of the host star which therefore make a negligible contribution to the offset. We measure abundances for Na and O that are consistent with solar to supersolar, with abundances relative to solar values of $21^{+27}_{-14}$ and $7^{+11}_{-4}$, respectively. We complement the transmission spectrum with new thermal emission constraints from Spitzer observations at 3.6 and 4.5 $\mu$m, which are best explained by the spectrum of an atmosphere with a temperature decreasing with altitude. A fit to the spectrum assuming an isothermal blackbody atmosphere constrains the dayside temperature to be Tp = 1545 ± 90 K.
iMaNGA: mock MaNGA galaxies based on IllustrisTNG and MaStar SSPs – I. Construction and analysis of the mock data cubes
Authors: Nanni Lorenza , Thomas Daniel , Trayford James , Maraston Claudia , Neumann Justus , Law David R , Hill Lewis , Pillepich Annalisa , Yan Renbin , Chen Yanping , Lazarz Dan
Published: June 2022

Galaxy formation and evolution simulations are essential tools to probe poorly known astrophysics processes, but particular care is needed to compare simulations with galaxy observations, as observed data need to be modelled as well. We present a method to generate mock galaxies from the hydro-dynamical IllustrisTNG simulations which are suited to compare with integral field spectroscopic observation of galaxies from the SDSS-IV/Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey. First, we include the same instrumental effects and procedures as adopted in the acquisition and analysis of real data. Furthermore, we generate the galaxy spectra from the simulations using new stellar population models based on the MaNGA stellar library (MaStar). In this way, our mock data cubes have the same spatial sampling, cover the same wavelength range (3600–10 300 Å), and share the same spectral resolution (R ≈ 1800) and flux calibration of real MaNGA galaxy spectra. In this first paper, we demonstrate the method over an early- and a late-type simulated galaxy from TNG50. We analyse the correspondent mock MaNGA-like data cubes with the same full spectral fitting code, firefly, which was used for the observed spectra. We find that the intrinsic and recovered age and metallicity gradients are consistent within 1σ, with residuals over all tassels consistent with 0 at the 68 ${{\ \rm per\ cent}}$ confidence level. We also perform the challenging test at comparing intrinsic and recovered star formation histories, finding a close resemblance between input and output. In follow-up papers, we will present a full simulated MaNGA-like catalogue (≈10 000 galaxies) with a comprehensive comparison of TNG50 simulations to MaNGA observational results.
PIPS, an advanced platform for period detection in time series – I. Fourier-likelihood periodogram and application to RR Lyrae stars
Authors: Murakami Yukei S , Jennings Connor , Hoffman Andrew M , Savel Arjun B , Sunseri James , Baer-Way Raphael , Stahl Benjamin E , Altunin Ivan , Girish Nachiket , Filippenko Alexei V
Published: June 2022

We describe the Period detection and Identification Pipeline Suite (pips) – a new, fast, and statistically robust platform for period detection and analysis of astrophysical time-series data. PIPS is an open-source Python package that provides various pre-implemented methods and a customizable framework for automated, robust period measurements with principled uncertainties and statistical significance calculations. In addition to detailing the general algorithm that underlies PIPS, this paper discusses one of PIPS’ central and novel features, the Fourier-likelihood periodogram, and compares its performance to existing methods. The resulting improved performance implies that one can construct deeper, larger, and more reliable sets of derived properties from various observations, including all-sky surveys. We present a comprehensive validation of PIPS against artificially generated data, which demonstrates the reliable performance of our algorithm for a class of periodic variable stars (RR Lyrae stars).
The galactic dust-up: modelling dust evolution in FIRE
Authors: Choban Caleb R , Kereš Dušan , Hopkins Philip F , Sandstrom Karin M , Hayward Christopher C , Faucher-Giguère Claude-André
Published: June 2022

Recent strides have been made developing dust evolution models for galaxy formation simulations but these approaches vary in their assumptions and degree of complexity. Here, we introduce and compare two separate dust evolution models (labelled ‘Elemental’ and ‘Species’), based on recent approaches, incorporated into the gizmo code and coupled with fire-2 stellar feedback and interstellar medium physics. Both models account for turbulent dust diffusion, stellar production of dust, dust growth via gas-dust accretion, and dust destruction from time-resolved supernovae, thermal sputtering in hot gas, and astration. The ‘Elemental’ model tracks the evolution of generalized dust species and utilizes a simple, ‘tunable’ dust growth routine, while the ‘Species’ model tracks the evolution of specific dust species with set chemical compositions and incorporates a physically motivated, two-phase dust growth routine. We test and compare these models in an idealized Milky Way-mass galaxy and find that while both produce reasonable galaxy-integrated dust-to-metals (D/Z) ratios and predict gas-dust accretion as the main dust growth mechanism, a chemically motivated model is needed to reproduce the observed scaling relation between individual element depletions and D/Z with column density and local gas density. We also find the inclusion of theoretical metallic iron and O-bearing dust species are needed in the case of specific dust species in order to match observations of O and Fe depletions, and the integration of a sub-resolution dense molecular gas/CO scheme is needed to both match observed C depletions and ensure carbonaceous dust is not overproduced in dense environments.
Recurrent Plant-Specific Duplications of KNL2 and its Conserved Function as a Kinetochore Assembly Factor
Authors: Zuo Sheng , Yadala Ramakrishna , Yang Fen , Talbert Paul , Fuchs Joerg , Schubert Veit , Ahmadli Ulkar , Rutten Twan , Pecinka Ales , Lysak Martin A , Lermontova Inna
Published: June 2022

KINETOCHORE NULL2 (KNL2) plays key role in the recognition of centromeres and new CENH3 deposition. To gain insight into the origin and diversification of the KNL2 gene, we reconstructed its evolutionary history in the plant kingdom. Our results indicate that the KNL2 gene in plants underwent three independent ancient duplications in ferns, grasses, and eudicots. Additionally, we demonstrated that previously unclassified KNL2 genes could be divided into two clades αKNL2 and βKNL2 in eudicots and γKNL2 and δKNL2 in grasses, respectively. KNL2s of all clades encode the conserved SANTA domain, but only the αKNL2 and γKNL2 groups additionally encode the CENPC-k motif. In the more numerous eudicot sequences, signatures of positive selection were found in both αKNL2 and βKNL2 clades, suggesting recent or ongoing adaptation. The confirmed centromeric localization of βKNL2 and mutant analysis suggests that it participates in loading of new CENH3, similarly to αKNL2. A high rate of seed abortion was found in heterozygous βknl2 plants and the germinated homozygous mutants did not develop beyond the seedling stage. Taken together, our study provides a new understanding of the evolutionary diversification of the plant kinetochore assembly gene KNL2, and suggests that the plant-specific duplicated KNL2 genes are involved in centromere and/or kinetochore assembly for preserving genome stability.
Allosteric couplings upon binding of RfaH to transcription elongation complexes
Authors: Molina José Alejandro , Galaz-Davison Pablo , Komives Elizabeth A , Artsimovitch Irina , Ramírez-Sarmiento César A
Published: June 2022

In every domain of life, NusG-like proteins bind to the elongating RNA polymerase (RNAP) to support processive RNA synthesis and to couple transcription to ongoing cellular processes. Structures of factor-bound transcription elongation complexes (TECs) reveal similar contacts to RNAP, consistent with a shared mechanism of action. However, NusG homologs differ in their regulatory roles, modes of recruitment, and effects on RNA synthesis. Some of these differences could be due to conformational changes in RNAP and NusG-like proteins, which cannot be captured in static structures. Here, we employed hydrogen-deuterium exchange mass spectrometry to investigate changes in local and non-local structural dynamics of Escherichia coli NusG and its paralog RfaH, which have opposite effects on expression of xenogenes, upon binding to TEC. We found that NusG and RfaH regions that bind RNAP became solvent-protected in factor-bound TECs, whereas RNAP regions that interact with both factors showed opposite deuterium uptake changes when bound to NusG or RfaH. Additional changes far from the factor-binding site were observed only with RfaH. Our results provide insights into differences in structural dynamics exerted by NusG and RfaH during binding to TEC, which may explain their different functional outcomes and allosteric regulation of transcriptional pausing by RfaH.
An in-library ligation strategy and its application in CRISPR/Cas9 screening of high-order gRNA combinations
Authors: Lu Zhike , Ni Ke , Wang Yingying , Zhou Yangfan , Li Yini , Yan Jianfeng , Song Qingkai , Liu Min , Xu Yujun , Yu Zhenxing , Guo Tiannan , Ma Lijia
Published: June 2022

Simultaneous targeting multiple genes is a big advantage of CRISPR (clustered regularly interspaced short palindromic repeats) genome editing but challenging to achieve in CRISPR screening. The crosstalk among genes or gene products is a common and fundamental mechanism to ensure cellular stability and functional diversity. However, the screening approach to map high-order gene combinations to the interesting phenotype is still lacking. Here, we developed a universal in-library ligation strategy and applied it to generate multiplexed CRISPR library, which could perturb four pre-designed targets in a cell. We conducted in vivo CRISPR screening for potential guide RNA (gRNA) combinations inducing anti-tumor immune responses. Simultaneously disturbing a combination of three checkpoints in CD8+ T cells was demonstrated to be more effective than disturbing Pdcd1 only for T cell activation in the tumor environment. This study developed a novel in-library ligation strategy to facilitate the multiplexed CRISPR screening, which could extend our ability to explore the combinatorial outcomes from coordinated gene behaviors.
iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families
Authors: Oteri Francesco , Sarti Edoardo , Nadalin Francesca , Carbone Alessandra
Published: June 2022

Residue coevolution within and between proteins is used as a marker of physical interaction and/or residue functional cooperation. Pairs or groups of coevolving residues are extracted from multiple sequence alignments based on a variety of computational approaches. However, coevolution signals emerging in subsets of sequences might be lost if the full alignment is considered. iBIS2Analyzer is a web server dedicated to a phylogeny-driven coevolution analysis of protein families with different evolutionary pressure. It is based on the iterative version, iBIS2, of the coevolution analysis method BIS, Blocks in Sequences. iBIS2 is designed to iteratively select and analyse subtrees in phylogenetic trees, possibly large and comprising thousands of sequences. With iBIS2Analyzer, openly accessible at http://ibis2analyzer.lcqb.upmc.fr/, the user visualizes, compares and inspects clusters of coevolving residues by mapping them onto sequences, alignments or structures of choice, greatly simplifying downstream analysis steps. A rich and interactive graphic interface facilitates the biological interpretation of the results.
The 2022 Ferno Award Address: CrEATE, an Efficient Crossover Evaluation of Addiction Treatment Efficacy
Authors: Perkins Kenneth A
Published: June 2022

Dozens of drugs have been evaluated in recent decades for initial evidence of efficacy to aid smoking cessation (i.e. “early Phase 2” testing, according to U.S. FDA terminology), with the vast majority failing to show efficacy. Even small randomized clinical trials (RCTs), the most common early Phase 2 tests, are costly undertakings, made more unappealing by their high likelihood of failure. At the same time, another early Phase 2 approach, acute tests of drug effects on surrogate endpoints such as withdrawal or craving severity, are more practical but have little predictive clinical validity. Described here is an innovative procedure that optimally combines the validity of clinical trials with the practical advantages of surrogate endpoint studies to more efficiently determine whether or not a novel drug warrants continued clinical development. This CrEATE procedure, or Crossover Evaluation of Addiction Treatment Efficacy, does so by assessing short-term quit success in smokers highly motivated to quit when briefly treated with active drug versus placebo in a crossover design, so that quit efficacy from both conditions is compared within participants. The program to develop and evaluate CrEATE demonstrates its sensitivity to efficacy from all three FDA-approved first-line cessation medications (NRT, varenicline, bupropion), tested here as model drugs, as well as specificity in identifying lack of efficacy with a drug known to be ineffective for cessation (modafinil). CrEATE has subsequently been used to evaluate a few novel interventions, concluding they lack efficacy in increasing quit success. Future directions for the potential utility of CrEATE are provided.

Implications: The ability of CrEATE to reach a Go/No Go decision more quickly and with far less cost lowers the risk of failure, meaning widespread use of the procedure should encourage the evaluation of more novel candidate drugs. With its greater efficiency, failed tests, unfortunately the most likely outcome in early Phase 2 studies, will cause less waste of resources. At the same time, CrEATE tests that indicate a novel treatment has efficacy will justify the substantial time and expense of moving forward to evaluate the drug in late Phase 2 RCTs.
Projected Effects of Disruptions to Human Immunodeficiency Virus (HIV) Prevention Services During the Coronavirus Disease 2019 Pandemic Among Black/African American Men Who Have Sex With Men in an Ending the HIV Epidemic Priority Jurisdiction
Authors: Labs Jennifer , Nunn Amy S , Chan Philip A , Bessey S , Park Carolyn J , Marshall Brandon D L , Patel Rupa R , Mena Leandro A , Goedel William C
Published: June 2022

Background

Disruptions in access to in-person human immunodeficiency virus (HIV) preventive care during the coronavirus disease 2019 (COVID-19) pandemic may have a negative impact on our progress towards the Ending the HIV Epidemic goals in the United States.

Methods

We used an agent-based model to simulate HIV transmission among Black/African American men who have sex with men in Mississippi over 5 years to estimate how different reductions in access affected the number of undiagnosed HIV cases, new pre-exposure prophylaxis (PrEP) starts, and HIV incidence.

Results

We found that each additional 25% decrease in HIV testing and PrEP initiation was associated with decrease of 20% in the number of cases diagnosed and 23% in the number of new PrEP starts, leading to a 15% increase in HIV incidence from 2020 to 2022.

Conclusions

Unmet need for HIV testing and PrEP prescriptions during the COVID-19 pandemic may temporarily increase HIV incidence in the years immediately after the disruption period.
Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon
Authors: Barros Jaime , Shrestha Him K , Serrani-Yarce Juan C , Engle Nancy L , Abraham Paul E , Tschaplinski Timothy J , Hettich Robert L , Dixon Richard A
Published: June 2022

Lignin biosynthesis begins with the deamination of phenylalanine and tyrosine (Tyr) as a key branch point between primary and secondary metabolism in land plants. Here, we used a systems biology approach to investigate the global metabolic responses to lignin pathway perturbations in the model grass Brachypodium distachyon. We identified the lignin biosynthetic protein families and found that ammonia-lyases (ALs) are among the most abundant proteins in lignifying tissues in grasses. Integrated metabolomic and proteomic data support a link between lignin biosynthesis and primary metabolism mediated by the ammonia released from ALs that is recycled for the synthesis of amino acids via glutamine. RNA interference knockdown of lignin genes confirmed that the route of the canonical pathway using shikimate ester intermediates is not essential for lignin formation in Brachypodium, and there is an alternative pathway from Tyr via sinapic acid for the synthesis of syringyl lignin involving yet uncharacterized enzymatic steps. Our findings support a model in which plant ALs play a central role in coordinating the allocation of carbon for lignin synthesis and the nitrogen available for plant growth. Collectively, these data also emphasize the value of integrative multiomic analyses to advance our understanding of plant metabolism.
WUSCHEL-related homeobox genes cooperate with cytokinin to promote bulbil formation in Lilium lancifolium
Authors: He Guoren , Cao Yuwei , Wang Jing , Song Meng , Bi Mengmeng , Tang Yuchao , Xu Leifeng , Ming Jun , Yang Panpan
Published: June 2022

The bulbil is an important vegetative reproductive organ in triploid tiger lily (Lilium lancifolium). Based on our previously obtained transcriptome data, we screened two WUSCHEL-related homeobox (WOX) genes closely related to bulbil formation, LlWOX9 and LlWOX11. However, the biological functions and regulatory mechanisms of LlWOX9 and LlWOX11 are unclear. In this study, we cloned the full-length coding sequences of LlWOX9 and LlWOX11. Transgenic Arabidopsis (Arabidopsis thaliana) showed increased branch numbers, and the overexpression of LlWOX9 and LlWOX11 in stem segments promoted bulbil formation, while the silencing of LlWOX9 and LlWOX11 inhibited bulbil formation, indicating that LlWOX9 and LlWOX11 are positive regulators of bulbil formation. Cytokinin type-B response regulators could bind to the promoters of LlWOX9 and LlWOX11 and promote their transcription. LlWOX11 could enhance cytokinin pathway signaling by inhibiting the transcription of type-A LlRR9. Our study enriches the understanding of the regulation of plant development by the WOX gene family and lays a foundation for further research on the molecular mechanism of bulbil formation in lily.
Vernalization attenuates dehydration tolerance in winter-annual Arabidopsis
Authors: Chen Lan , Hu Pengcheng , Lu Qianqian , Zhang Fei , Su Yanhua , Ding Yong
Published: June 2022

In winter-annual plants, exposure to cold temperatures induces cold tolerance and accelerates flowering in the following spring. However, little is known about plant adaptations to dehydration stress after winter. Here, we found that dehydration tolerance is reduced in winter-annual Arabidopsis (Arabidopsis thaliana) after vernalization. Winter-annual Arabidopsis plants with functional FRIGIDA (FRI) exhibited high dehydration tolerance, with small stomatal apertures and hypersensitivity to exogenous abscisic acid. Dehydration tolerance and FLOWERING LOCUS C (FLC) transcript levels gradually decreased with prolonged cold exposure in FRI plants. FLC directly bound to the promoter of OPEN STOMATA1 (OST1) and activated OST1 expression. Loss of FLC function resulted in decreased dehydration tolerance and reduced OST1 transcript levels. FLC and OST1 act in the same dehydration stress pathway, with OST1 acting downstream of FLC. Our study provides insights into the mechanisms by which FRI modulates dehydration tolerance through the FLC–OST1 module. Our results suggest that winter-annual Arabidopsis integrates dehydration tolerance and flowering time to adapt to environmental changes from winter to spring.
The Brassicaceae genome resource (TBGR): A comprehensive genome platform for Brassicaceae plants
Authors: Liu Zhuo , Li Nan , Yu Tong , Wang Zhiyuan , Wang Jiaqi , Ren Jun , He Jinghua , Huang Yini , Shi Keqian , Yang Qihang , Wu Tong , Lin Hao , Song Xiaoming
Published: June 2022

The Brassicaceae is an important plant family. We built a user-friendly, web-based, comparative, and functional genomic database, The Brassicaceae Genome Resource (TBGR, http://www.tbgr.org.cn), based on 82 released genomes from 27 Brassicaceae species. The TBGR database contains a large number of important functional genes, including 4,096 glucosinolate genes, 6,625 auxin genes, 13,805 flowering genes, 36,632 resistance genes, 1,939 anthocyanin genes, and 1,231 m6A genes. A total of 1,174,049 specific guide sequences for clustered regularly interspaced short palindromic repeats and 5,856,479 transposable elements were detected in Brassicaceae. TBGR also provides information on synteny, duplication, and orthologs for 27 Brassicaceae species. The TBGR database contains 1,183,851 gene annotations obtained using the TrEMBL, Swiss-Prot, Nr, GO, and Pfam databases. The BLAST, Synteny, Primer Design, Seq_fetch, and JBrowse tools are provided to help users perform comparative genomic analyses. All the genome assemblies, gene models, annotations, and bioinformatics results can be easily downloaded from the TBGR database. We plan to improve and continuously update the database with newly assembled genomes and comparative genomic studies. We expect the TBGR database to become a key resource for the study of the Brassicaceae.
A natural antisense RNA improves chrysanthemum cold tolerance by regulating the transcription factor DgTCP1
Authors: Li Xin , Yang Qing , Liao Xiaoqin , Tian Yuchen , Zhang Fan , Zhang Lei , Liu Qinglin
Published: June 2022

Long noncoding RNAs (lncRNAs) are widely involved in the regulation of plant growth and development, but their mechanism of action in response to cold stress in plants remains unclear. Here, we found an lncRNA transcribed from the antisense strand of DgTCP1 (class I Teosinte branched1/Cycloidea/Proliferating [TCP] transcription factor) of chrysanthemum (Chrysanthemum morifolium Ramat.), named DglncTCP1. During the response of chrysanthemum to cold stress, overexpression of DgTCP1 improved the cold tolerance of chrysanthemum, while the DgTCP1 editing line (dgtcp1) showed decreased tolerance to cold stress. Overexpression of DglncTCP1 also increased the cold tolerance of chrysanthemum, while the DglncTCP1 amiRNA lines (DglncTCP1 amiR-18/38) also showed decreased tolerance to cold stress. Additionally, the overexpression of DglncTCP1 upregulated the expression of DgTCP1. This indicated that DglncTCP1 may play a cis-regulatory role in the regulatory process of DgTCP1 in cold tolerance. DglncTCP1 acts as a scaffold to recruit the histone modification protein DgATX (ARABIDOPSIS TRITHORAX from chrysanthemum) to DgTCP1 to enhance H3K4me3 levels, thereby activating DgTCP1 expression. Moreover, DgTCP1 can directly target DgPOD (peroxidase gene from chrysanthemum) to promote its expression and reduce reactive oxygen species accumulation, thereby improving the cold tolerance of chrysanthemum. In conclusion, these results suggest that natural antisense lncRNA plays a key role in improving the cold tolerance of chrysanthemum.
Arabidopsis MAPKK kinases YODA, MAPKKK3, and MAPKKK5 are functionally redundant in development and immunity
Authors: Wang Yiping , Wu Yingying , Zhang Hailei , Wang Pengxi , Xia Yiji
Published: June 2022

Three MAPK cascade components in Arabidopsis, YDA (MAPKKK4) and MAPKKK3/5, function redundantly in multiple developmental processes and immunity and regulate floral organ abscission.
Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa
Authors: Gao Yubang , Liu Xuqing , Jin Yandong , Wu Ji , Li Shuang , Li Yaxing , Chen Binqing , Zhang Yaxin , Wei Linxiao , Li Wei , Li Ruili , Lin Chentao , Reddy Anireddy S N , Jaiswal Pankaj , Gu Lianfeng
Published: June 2022

Understanding gene expression and regulation requires insights into RNA transcription, processing, modification, and translation. However, the relationship between the epitranscriptome and the proteome under drought stress remains undetermined in poplar (Populus trichocarpa). In this study, we used Nanopore direct RNA sequencing and tandem mass tag-based proteomic analysis to examine epitranscriptomic and proteomic regulation induced by drought treatment in stem-differentiating xylem (SDX). Our results revealed a decreased full-length read ratio under drought treatment and, especially, a decreased association between transcriptome and proteome changes in response to drought. Epitranscriptome analysis of cellulose- and lignin-related genes revealed an increased N6-Methyladenosine (m6A) ratio, which was accompanied by decreased RNA abundance and translation, under drought stress. Interestingly, usage of the distal poly(A) site increased during drought stress. Finally, we found that transcripts of highly expressed genes tend to have shorter poly(A) tail length (PAL), and drought stress increased the percentage of transcripts with long PAL. These findings provide insights into the interplay among m6A, polyadenylation, PAL, and translation under drought stress in P. trichocarpa SDX.
Coherent polaron dynamics of electrons solvated in polar liquids
Authors: Singh Poonam , Zhang Jia , Ghalgaoui Ahmed , Reimann Klaus , Fingerhut Benjamin P , Woerner Michael , Elsaesser Thomas
Published: June 2022

An electron solvated in a polar liquid is an elementary quantum system with properties governed by electric interactions with a fluctuating molecular environment. In the prevailing single particle picture, the quantum ground and excited states are determined by a self-consistent potential, as defined by the particular local configuration of the solvation shell. This description neglects collective many-body excitations, which arise from the coupling of electronic degrees of freedom and nuclear motions of the environment. While recent experiments have demonstrated collective nonequilbrium electronic–nuclear motion, i.e. polaron excitations in liquid water, their relevance in the broader context of polar liquids has remained unexplored. Here, we study the nonequilibrium dielectric response of the, compared to water, less polar alcohols isopropanol, and ethylene glycol, that also display a different hydrogen bond pattern. We demonstrate that ultrafast relaxation of photogenerated electrons impulsively induces coherent charge oscillations, which persist for some 10 ps. They emit electric waves in a frequency range from 0.1 to 2 THz, depending on electron concentration. Oscillation frequencies and line shapes are reproduced by a unified polaron picture for alcohols and water, which is based on a Clausius–Mossotti local field approach for the THz dielectric function. The analysis suggests a longitudinal character of many-body polaron excitations and a weak coupling to transverse excitations, supported by the underdamped character of charge oscillations. Polaron dynamics are governed by the long-range Coulomb interaction between an excess electron and several thousands of polar solvent molecules, while local electron solvation geometries play a minor role.
Gains in Daily Stepping Activity in People With Chronic Stroke After High-Intensity Gait Training in Variable Contexts
Authors: Hornby T George , Plawecki Abbey , Lotter Jennifer K , Scofield Molly E , Lucas Emily , Henderson Christopher E
Published: June 2022

Objective

Many physical therapist interventions provided to individuals with chronic stroke can lead to gains in gait speed or endurance (eg, 6-Minute Walk Test [6MWT]), although changes in objective measures of participation are not often observed. The goal of this study was to determine the influence of different walking interventions on daily stepping (steps per day) and the contributions of demographic, training, and clinical measures to these changes.

Methods

In this secondary analysis of a randomized clinical trial, steps per day at baseline and changes in steps per day following 1 of 3 locomotor interventions were evaluated in individuals who were ambulatory and >6 months after stroke. Data were collected on 58 individuals who received ≤30 sessions of high-intensity training (HIT) in variable contexts (eg, tasks and environments; n = 19), HIT focused on forward walking (n = 19), or low-intensity variable training (n = 20). Primary outcomes were steps per day at baseline, at post-training, and at a 3-month follow-up, and secondary outcomes were gait speed, 6MWT, balance, and balance confidence. Correlation and regression analyses identified demographic and clinical variables associated with steps per day.

Results

Gains in steps per day were observed across all groups combined, with no between-group differences; post hoc within-group analyses revealed significant gains only following HIT in variable contexts. Both HIT groups showed gains in endurance (6MWT), with increases in balance confidence only following HIT in variable contexts. Changes in steps per day were associated primarily with gains in 6MWT, with additional associations with baseline 6MWT, lower-extremity Fugl-Meyer scores, and changes in balance confidence.

Conclusion

HIT in variable contexts elicited gains in daily stepping, with changes primarily associated with gains in gait endurance.

Impact

Providing HIT in variable contexts appears to improve measures of participation (eg, daily stepping) that may be associated with clinical measures of function. Gains in multiple measures of mobility and participation with HIT in variable contexts may improve the efficiency and value of physical therapy services.
Lasiodiplodia iraniensis, a New Causal Agent of Tuber Rot on Yam (Dioscorea Species) Imported into the United States and Implications for Quarantine Decisions
Authors: Jibrin Mustafa Ojonuba , Liu Qingchun , Huang Yi , Urbina Hector , Gazis Romina , Zhang Shouan
Published: June 2022

One negative consequence of international trade of agricultural commodities is the inadvertent global spread of crop diseases. Yam (Dioscorea spp.) is a staple food crop in many countries and is traded globally. Most of the commercially traded yams in the United States are imported. In late 2020, samples of yam tubers from a commercial facility were submitted to the plant diagnostic clinic at the UF/IFAS Tropical Research and Education Center in Homestead, Florida. Samples showed rotten symptoms and were drawn from lots that were marked to be destroyed because the source of the rotting symptoms was unknown. Preliminary isolation showed that a fungus was consistently associated with the symptoms and was confirmed in the subsequent pathogenicity test as the causal agent. The fungus grew profusely on potato dextrose agar (PDA) with highly melanized hyphae. Matured conidia showed longitudinal striations. Based on its growth pattern and morphology, it was suspected that this fungus may be in the genus Lasiodiplodia. DNA-based identification using partial sequences of the internal transcribed spacer (ITS), β-tubulin (TUB2), 28S rDNA (LSU), and elongation factor alpha (EF1-α) genes confirmed the identity of the isolates as Lasiodiplodia iraniensis Abdollahz., Zare & A.J.L. Phillips (synonym: L. iranensis). This is the first report of L. iraniensis affecting yam and has implications for international trade. This finding will provide an important foundation for making quarantine decisions to prevent spread of this disease.
Evaluation of Thousand Cankers Disease-Symptomatic Juglans nigra in Southwestern Ohio Following Population Collapse of Pityophthorus juglandis
Authors: Juzwik Jennifer , McDermott-Kubeczko Margaret E. , Moore Melanie J. , Ginzel Matthew
Published: June 2022

Mass attacks of Juglans nigra by Pityophthorus juglandis and its introduction of the canker pathogen Geosmithia morbida lead to branch dieback and, commonly, tree death in locations with outbreaks of thousand cankers disease (TCD). Following initial detection of TCD in Butler County, Ohio, in 2012, and trapping of thousands of P. juglandis, a dramatic decrease in insect population occurred. Dissections of “lingering” TCD-symptomatic J. nigra in 2014 and 2015 were conducted to document the presence of “typical” Geosmithia cankers and other types of damage on branches and main stems. Isolation and subsequent molecular identification of G. morbida and other selected fungi were attempted from representatives of the various canker-like and insect-associated damage observed. Of the fungi obtained, G. morbida was most commonly isolated, primarily from “typical” Geosmithia cankers, but it was also obtained at lower frequencies from other damage types. In addition, G. morbida commonly co-occurred with Fusarium solani ( F. solani species complex) but infrequently with Diplodia seriata. These other fungal species could contribute to the severity of canker development. These results suggest that the TCD pathogen persists in the landscape following population collapse of the primary insect vector and would be of interest to state regulatory agencies in the eastern United States.
Racial and ethnic disparities in access to gynecologic care
Authors: Mercier Ann Marie , Carter Stormie R. , Manning Nirvana
Published: June 2022

Purpose of review

Despite efforts to minimize patient barriers to equitable care, health disparities persist in gynecology. This paper seeks to highlight racial and ethnic disparities in gynecologic care as represented by recent literature.

Recent findings

Disparities exist among many areas including preventive screenings, vaccination rates, contraception use, infertility, and oncologic care. These can be identified at the patient, physician, and institutional levels.

As we identify these social disparities in healthcare, we gain valuable knowledge of where our efforts are lacking and where we can further improve the health of women. Future research should focus on identifying and combating such disparities with measurable changes in health outcomes.
Limited English proficiency in the labor and delivery unit
Authors: Togioka Brandon M. , Seligman Katherine M. , Delgado Carlos M.
Published: June 2022

Purpose of review

Limited English proficiency (LEP) impacts patient access to safe and comprehensive care during the antepartum, intrapartum, and postpartum periods. In this review, we explore disparities in care delivery and outcomes that LEP women experience, and discuss the importance of providing language concordant care and using interpretation services appropriately.

Recent findings

The number of individuals with LEP is steadily increasing in the United States. Pregnant women with LEP suffer disparities in obstetric care and are at risk for postpartum depression, breastfeeding difficulties, and substandard newborn care after neonatal ICU discharge because of insufficient education. Addressing these issues requires the implementation of language concordant care and education, along with the utilization of medically trained interpreters. Although further evidence is needed, the authors support these interventions to improve patient satisfaction, decrease medical errors, and curtail misdiagnoses.

The pregnant woman with limited English proficiency is at risk of receiving suboptimal care and experiencing negative outcomes during the antepartum, intrapartum, and postpartum periods. The use of medically trained interpreters and the provision of language concordant care, through workforce diversification and the creation of forms and educational materials in diverse languages, can improve patient safety, outcomes, and quality of care.
Medical disease and ambulatory surgery, new insights in patient selection based on medical disease
Authors: Fuchs-Buder Thomas , Rosenberg Jacob
Published: June 2022

Purpose of review

Improvements in perioperative care contributed to enlarge the eligibility criteria for day case surgery and more and more patients with comorbidities may be concerned. However, underlying medical diseases may influence postoperative outcomes, and therefore, must be considered when selecting patients to undergo ambulatory surgery.

Recent findings

To limit postoperative complications, rigid patient selection criteria are often applied in ambulatory surgery. In practice, however, most of these criteria predict the occurrence of treatable perioperative adverse events but not the need for unanticipated admission or readmission.

The underlying medical diseases should not be considered as sole criteria but they should rather be regarded as a dynamic process, which includes the surgical procedure as well as the experience and expertise of the perioperative setting.
How to optimize the perioperative care of patients with orphan diseases: what the anesthesiologist needs to know
Authors: Peck Jacquelin , Firth Paul G.
Published: June 2022

Purpose of review

Despite a very low individual prevalence, rare or orphan diseases are estimated to collectively affect as much as 6–8% of the general population. These diseases provide a challenge to anesthetic delivery because of the lack of evidence to guide optimal management.

Recent findings

The expansion of information technology has made facts about individual orphan diseases easier to find. Several reputable websites, hosted variously by anesthetic societies, rare disease organizations, and government agencies, provide information about rare diseases and anesthetic management.

Improved access to resources of knowledge may allow for more informed anesthetic management of orphan diseases. The combination of a thorough review of existing knowledge about individual diseases and a structured anesthetic assessment may assist in the delivery of well tolerated anesthetic care of rare conditions.
Causes of health inequities
Authors: Lee Allison , Padilla Cesar
Published: June 2022

Purpose of review

A renewed focus on U.S. racial and ethnic maternal health disparities has arisen following high-profile incidents of police violence and antiracism protests which coincided with the coronavirus disease 2019 pandemic, which has exerted a disproportionate effect on minority communities. Understanding the causes of disparities is pivotal for developing solutions.

Recent findings

Social determinants of health must be addressed during clinical care; however, race must be used with caution in clinical decision-making. Medicaid expansion has been associated with a decrease in severe maternal morbidity and mortality, especially for racial and ethnic minority women. Indirect obstetric causes are the leading cause of maternal death.

Policy-level changes and investment in marginalized communities are required to improve access to quality maternity care at all stages, including preconception, interconception, prenatal, intrapartum and postpartum for 12 months after delivery. Improvements in hospital quality and implementation of evidence-based bundles of care are crucial. Clinicians should receive training regarding susceptibility to implicit bias. To support the research agenda, better collection of race and ethnicity data and anesthesia care indicators is a priority (see Video, Supplemental Digital Content 1 {Video abstract that provides an overview of the causes racial and ethnic disparities in maternal health outcomes.} http://links.lww.com/COAN/A85).