bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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

Abstract
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

Abstract
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

Abstract
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

AbstractResidue 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

AbstractDozens 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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.