bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pyrethroid Susceptibility in Field Populations of Picture-Winged Flies (Diptera: Ulidiidae) Infesting Fresh Market Sweet Corn in Florida
Authors: Schwan Resende Eric , Beuzelin Julien M , Dunkley Victoria E , Paula-Moraes Silvana V , Seal Dakshina R , Nuessly Gregg S 
Published: August 2022

Abstract
Picture-winged flies (Diptera: Ulidiidae) are the most damaging insect pests of sweet corn (Zea mays L.) produced in Florida for the fresh market. Management of these pests, referred to as corn silk flies, relies on frequent pyrethroid applications targeting adults. In response to the need for an insecticide resistance management (IRM) program for corn silk flies in this highly intensive crop system, glass vial bioassays were conducted to determine the susceptibility of 12 corn silk fly populations to the pyrethroid beta-cyfluthrin. Two Euxesta eluta Loew and nine Euxesta stigmatias Loew populations were obtained by collecting infested ears in commercial and experimental fields in 2020 and 2021. One E. eluta laboratory colony was used as a susceptible reference population. The E. eluta reference colony was the most susceptible population, with an LC50 value of 0.01 µg/vial. The E. stigmatias field populations were generally less susceptible to beta-cyfluthrin than the E. eluta field populations, with the highest LC50 values attaining 3.51 µg/vial and 0.19 µg/vial, respectively. In addition, the five E. stigmatias populations from commercial sweet corn fields were as much as 17.6 times less susceptible than the four E. stigmatias populations from nontreated fields. Results suggest that E. stigmatias is less susceptible to pyrethroids than E. eluta. Results also suggest that corn silk flies in commercial sweet corn fields are selected for reduced pyrethroid susceptibility throughout the growing season. This study successfully used the glass vial bioassay method for corn silk flies, providing a new tool to initiate an IRM program.
Observing EAGLE galaxies with JWST: predictions for Milky Way progenitors and their building blocks
Authors: Evans Tilly A , Fattahi Azadeh , Deason Alis J , Frenk Carlos S 
Published: August 2022

ABSTRACT
We present predictions, derived from the EAGLE ΛCDM cosmological hydrodynamical simulations, for the abundance and properties of galaxies expected to be detected at high redshift by the James Webb Space Telescope (JWST). We consider the galaxy population as a whole and focus on the sub-population of progenitors of Milky Way (MW) analogues, defined to be galaxies with accretion histories similar to the MW’s, that is, galaxies that underwent a merger resembling the Gaia-Enceladus-Sausage (GES) event and that contain an analogue of the Large Magellanic Cloud (LMC) satellite today. We derive the luminosity function of all EAGLE galaxies in JWST/NIRCam passbands, in the redshift range z = 2 − 8, taking into account dust obscuration and different exposure times. For an exposure time of T = 105s, average MW progenitors are observable as far back as z ∼ 6 in most bands, and this changes to z ∼ 5 and z ∼ 4 for the GES and LMC progenitors, respectively. The progenitors of GES and LMC analogues are, on average, ∼2 and ∼1 mag fainter than the MW progenitors at most redshifts. They lie, on average, within ∼60 and 30 arcsec, respectively, of their future MW host at all times, and thus will appear within the field of view of JWST/NIRCam. We conclude that galaxies resembling the main progenitor of the MW and its major accreted components should be observable with JWST beyond redshift 2, providing a new and unique window in studying the formation history of our own galaxy.
SOFIA/HAWC+ observations of the Crab Nebula: dust properties from polarized emission
Authors: Chastenet Jérémy , De Looze Ilse , Hensley Brandon S , Vandenbroucke Bert , Barlow Mike J , Rho Jeonghee , Ravi Aravind P , Gomez Haley L , Kirchschlager Florian , Macías-Pérez Juan , Matsuura Mikako , Pattle Kate , Ponthieu Nicolas , Priestley Felix D , Relaño Monica , Ritacco Alessia , Wesson Roger 
Published: August 2022

ABSTRACT
Supernova remnants (SNRs) are well-recognized dust producers, but their net dust production rate remains elusive due to uncertainties in grain properties that propagate into observed dust mass uncertainties, and determine how efficiently these grains are processed by reverse shocks. In this paper, we present a detection of polarized dust emission in the Crab pulsar wind nebula, the second SNR with confirmed polarized dust emission after Cassiopeia A. We constrain the bulk composition of the dust with new SOFIA/HAWC+ polarimetric data in band C 89 μm and band D 154 μm. After correcting for synchrotron polarization, we report dust polarization fractions ranging between 3.7–9.6 per cent and 2.7–7.6 per cent in three individual dusty filaments at 89 and 154 μm, respectively. The detected polarized signal suggests the presence of large (≳0.05–0.1 μm) grains in the Crab Nebula. With the observed polarization, and polarized and total fluxes, we constrain the temperatures and masses of carbonaceous and silicate grains. We find that the carbon-rich grain mass fraction varies between 12 and 70 per cent, demonstrating that carbonaceous and silicate grains co-exist in this SNR. Temperatures range from ∼40 to ∼70 K and from ∼30 to ∼50 K for carbonaceous and silicate grains, respectively. Dust masses range from ∼10−4 to ∼10−2 M⊙ for carbonaceous grains and to ∼10−1 M⊙ for silicate grains, in three individual regions.
Still at odds with conventional galaxy evolution: the star formation history of ultradiffuse galaxy Dragonfly 44
Authors: Webb Kristi A , Villaume Alexa , Laine Seppo , Romanowsky Aaron J , Balogh Michael , van Dokkum Pieter , Forbes Duncan A , Brodie Jean , Martin Christopher , Matuszewski Matt 
Published: August 2022

ABSTRACT
We study the star formation history (SFH) of the ultradiffuse galaxy (UDG) Dragonfly 44 (DF44) based on the simultaneous fit to near-ultraviolet to near-infrared photometry and high signal-to-noise optical spectroscopy. In fitting the observations, we adopt an advanced physical model with a flexible SFH and discuss the results in the context of the degeneracies between stellar population parameters. Through reconstructing the mass-assembly history with a prior for extended star formation (SF) (akin to methods in the literature), we find that DF44 formed 90 per cent of its stellar mass by z ∼ 0.9 (∼7.2 Gyr ago). In comparison, using a prior that prefers concentrated SF (as informed by previous studies of DF44’s stellar populations) suggests that DF44 formed as early as z ∼ 8 (∼12.9 Gyr ago). Regardless of whether DF44 is old or very old, the SFHs imply early SF and rapid quenching. This result, together with DF44’s large size and evidence that it is on its first infall into the Coma cluster, challenges UDG formation scenarios from simulations that treat all UDGs as contiguous with the canonical dwarf population. While our results cannot confirm any particular formation scenario, we can conclude from this that DF44 experienced a rare quenching event.
The SAMI Galaxy Survey: Using concentrated star formation and stellar population ages to understand environmental quenching
Authors: Wang(王迪) Di , Croom Scott M , Bryant Julia J , Vaughan Sam P , Schaefer Adam L , D’Eugenio Francesco , Barsanti Stefania , Brough Sarah , Lagos Claudia del P , Medling Anne M , Oh Sree , van de Sande Jesse , Santucci Giulia , Bland-Hawthorn Joss , Goodwin Michael , Groves Brent , Lawrence Jon , Owers Matt S , Richards Samuel 
Published: August 2022

ABSTRACT
We study environmental quenching using the spatial distribution of current star formation and stellar population ages with the full SAMI Galaxy Survey. By using a star formation concentration index [C-index, defined as log10(r50, H α/r50, cont)], we separate our sample into regular galaxies (C-index ≥−0.2) and galaxies with centrally concentrated star formation (SF-concentrated; C-index &lt;−0.2). Concentrated star formation is a potential indicator of galaxies currently undergoing ‘outside-in’ quenching. Our environments cover ungrouped galaxies, low-mass groups (M200 ≤ 1012.5M⊙), high-mass groups (M200 in the range 1012.5–14 M⊙) and clusters (M200 &gt; 1014M⊙). We find the fraction of SF-concentrated galaxies increases as halo mass increases by 9 ± 2 per cent, 8 ± 3 per cent, 19 ± 4 per cent, and 29 ± 4 per cent for ungrouped galaxies, low-mass groups, high-mass groups, and clusters, respectively. We interpret these results as evidence for ‘outside-in’ quenching in groups and clusters. To investigate the quenching time-scale in SF-concentrated galaxies, we calculate light-weighted age (AgeL) and mass-weighted age (AgeM) using full spectral fitting, as well as the Dn4000 and HδA indices. We assume that the average galaxy age radial profile before entering a group or cluster is similar to ungrouped regular galaxies. At large radius (1–2 Re), SF-concentrated galaxies in high-mass groups have older ages than ungrouped regular galaxies with an age difference of 1.83 ± 0.38 Gyr for AgeL and 1.34 ± 0.56 Gyr for AgeM. This suggests that while ‘outside-in’ quenching can be effective in groups, the process will not quickly quench the entire galaxy. In contrast, the ages at 1–2 Re of cluster SF-concentrated galaxies and ungrouped regular galaxies are consistent (difference of 0.19 ± 0.21 Gyr for AgeL, 0.40 ± 0.61 Gyr for AgeM), suggesting the quenching process must be rapid.
Simulations of astrometric planet detection in Alpha Centauri by intensity interferometry
Authors: Rai Km Nitu , Sarangi Subrata , Saha Prasenjit , Basak Soumen 
Published: August 2022

ABSTRACT
Recent dynamical studies indicate that the possibility of an Earth-like planet around α Cen A or B should be taken seriously. Such a planet, if it exists, would perturb the orbital astrometry by $\lt {10}\, {\mu {\rm as}}$, which is 10−6 of the separation between the two stars. We assess the feasibility of detecting such perturbations using ground-based intensity interferometry. We simulate a dedicated set-up consisting of four 40-cm telescopes equipped with photon counters and correlators with a time resolution of $0.1\, \rm ns$, and a sort of matched filter implemented through an aperture mask. The astrometric error from one night of observing α Cen AB is $\approx 0.5\, \rm mas$. The error decreases if longer observing times and multiple spectral channels are used, as (channels × nights)−1/2.
The Genomic Basis of Evolutionary Novelties in a Leafhopper
Authors: Li Zheng , Li Yiyuan , Xue Allen Z , Dang Vy , Holmes V Renee , Johnston J Spencer , Barrick Jeffrey E , Moran Nancy A 
Published: August 2022

Abstract
Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the glassy-winged sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS and then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory.
Safety and efficacy of switching immunosuppressive drugs for maintenance treatment in patients with systemic lupus erythematosus: A retrospective cohort study
Authors: Ayano Masahiro , Kimoto Yasutaka , Mitoma Hiroki , Akahoshi Mitsuteru , Ono Nobuyuki , Arinobu Yojiro , Akashi Koichi , Horiuchi Takahiko , Niiro Hiroaki 
Published: August 2022

ABSTRACT

Objectives
We aim to clarify the efficacy and safety of switching immunosuppressive drugs and to identify the predictive factors for treatment failure after switching in patients with systemic lupus erythematosus (SLE).

Methods
We retrospectively evaluated patients with SLE who switched immunosuppressive drugs for any reason in our hospital between 2015 and 2020. The efficacy endpoints were the change in SLE Disease Activity Index 2000 score, prednisolone dose, and disease status over 12 months, as well as treatment continuation rates. The safety endpoint was the frequency of adverse events over 1 year before and after switching. Cox hazard regression analyses were used to identify the predictive factors for treatment failure.

Results
Thirty-nine patients (age, 41.5 ± 12.6 years; 35 women and 4 men) were analysed. The SLE Disease Activity Index score and prednisolone dose were significantly reduced after switching, with few disease exacerbations over 12 months. The 1- and 2-year continuation rates were 71.4% and 62.3%, respectively. The frequency of adverse events was similar in the year before and after switching the drug. Drug switching due to inadequate efficacy was a predictive factor of less likely treatment failure.

Conclusions
Immunosuppressive drug switching led to reduced disease activity and decreased glucocorticoid dose without disease exacerbations and severe adverse events.
PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins
Authors: Laverty Kaitlin U , Jolma Arttu , Pour Sara E , Zheng Hong , Ray Debashish , Morris Quaid , Hughes Timothy R 
Published: August 2022

Abstract
Modelling both primary sequence and secondary structure preferences for RNA binding proteins (RBPs) remains an ongoing challenge. Current models use varied RNA structure representations and can be difficult to interpret and evaluate. To address these issues, we present a universal RNA motif-finding/scanning strategy, termed PRIESSTESS (Predictive RBP-RNA InterpretablE Sequence-Structure moTif regrESSion), that can be applied to diverse RNA binding datasets. PRIESSTESS identifies dozens of enriched RNA sequence and/or structure motifs that are subsequently reduced to a set of core motifs by logistic regression with LASSO regularization. Importantly, these core motifs are easily visualized and interpreted, and provide a measure of RBP secondary structure specificity. We used PRIESSTESS to interrogate new HTR-SELEX data for 23 RBPs with diverse RNA binding modes and captured known primary sequence and secondary structure preferences for each. Moreover, when applying PRIESSTESS to 144 RBPs across 202 RNA binding datasets, 75% showed an RNA secondary structure preference but only 10% had a preference besides unpaired bases, suggesting that most RBPs simply recognize the accessibility of primary sequences.
Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory
Authors: Abdulla Amith Z , Vaillant Cédric , Jost Daniel 
Published: August 2022

Abstract
In eukaryotes, many stable and heritable phenotypes arise from the same DNA sequence, owing to epigenetic regulatory mechanisms relying on the molecular cooperativity of ‘reader–writer’ enzymes. In this work, we focus on the fundamental, generic mechanisms behind the epigenome memory encoded by post-translational modifications of histone tails. Based on experimental knowledge, we introduce a unified modeling framework, the painter model, describing the mechanistic interplay between sequence-specific recruitment of chromatin regulators, chromatin-state-specific reader–writer processes and long-range spreading mechanisms. A systematic analysis of the model building blocks highlights the crucial impact of tridimensional chromatin organization and state-specific recruitment of enzymes on the stability of epigenomic domains and on gene expression. In particular, we show that enhanced 3D compaction of the genome and enzyme limitation facilitate the formation of ultra-stable, confined chromatin domains. The model also captures how chromatin state dynamics impact the intrinsic transcriptional properties of the region, slower kinetics leading to noisier expression. We finally apply our framework to analyze experimental data, from the propagation of γH2AX around DNA breaks in human cells to the maintenance of heterochromatin in fission yeast, illustrating how the painter model can be used to extract quantitative information on epigenomic molecular processes.
Domain specific mutations in dyskerin disrupt 3′ end processing of scaRNA13
Authors: Nagpal Neha , Tai Albert K , Nandakumar Jayakrishnan , Agarwal Suneet 
Published: August 2022

Abstract
Mutations in DKC1 (encoding dyskerin) cause telomere diseases including dyskeratosis congenita (DC) by decreasing steady-state levels of TERC, the non-coding RNA component of telomerase. How DKC1 mutations variably impact numerous other snoRNAs remains unclear, which is a barrier to understanding disease mechanisms in DC beyond impaired telomere maintenance. Here, using DC patient iPSCs, we show that mutations in the dyskerin N-terminal extension domain (NTE) dysregulate scaRNA13. In iPSCs carrying the del37L NTE mutation or engineered to carry NTE mutations via CRISPR/Cas9, but not in those with C-terminal mutations, we found scaRNA13 transcripts with aberrant 3′ extensions, as seen when the exoribonuclease PARN is mutated in DC. Biogenesis of scaRNA13 was rescued by repair of the del37L DKC1 mutation by genome-editing, or genetic or pharmacological inactivation of the polymerase PAPD5, which counteracts PARN. Inspection of the human telomerase cryo-EM structure revealed that in addition to mediating intermolecular dyskerin interactions, the NTE interacts with terminal residues of the associated snoRNA, indicating a role for this domain in 3′ end definition. Our results provide mechanistic insights into the interplay of dyskerin and the PARN/PAPD5 axis in the biogenesis and accumulation of snoRNAs beyond TERC, broadening our understanding of ncRNA dysregulation in human diseases.
DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
Authors: Barissi Sandro , Sala Alba , Wieczór Miłosz , Battistini Federica , Orozco Modesto 
Published: August 2022

Abstract
We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can be extended to epigenetic variants, mismatches, mutations, or any non-coding nucleobases. When complemented with chromatin structure information, our in vitro trained method provides also good estimates of in vivo binding sites in yeast.
ADP-ribosylation of RNA in mammalian cells is mediated by TRPT1 and multiple PARPs
Authors: Weixler Lisa , Feijs Karla L H , Zaja Roko 
Published: August 2022

Abstract
RNA function relies heavily on posttranscriptional modifications. Recently, it was shown that certain PARPs and TRPT1 can ADP-ribosylate RNA in vitro. Traditionally, intracellular ADP-ribosylation has been considered mainly as a protein posttranslational modification. To date, it is not clear whether RNA ADP-ribosylation occurs in cells. Here we present evidence that different RNA species are ADP-ribosylated in human cells. The modification of cellular RNA is mediated by several transferases such as TRPT1, PARP10, PARP11, PARP12 and PARP15 and is counteracted by different hydrolases including TARG1, PARG and ARH3. In addition, diverse cellular stressors can modulate the content of ADP-ribosylated RNA in cells. We next investigated potential consequences of ADP-ribosylation for RNA and found that ADPr-capped mRNA is protected against XRN1 mediated degradation but is not translated. T4 RNA ligase 1 can ligate ADPr-RNA in absence of ATP, resulting in the incorporation of an abasic site. We thus provide the first evidence of RNA ADP-ribosylation in mammalian cells and postulate potential functions of this novel RNA modification.
Riboflavin intake and status and relationship to anemia
Authors: Aljaadi Abeer M , Devlin Angela M , Green Tim J 
Published: August 2022

AbstractRiboflavin in its coenzyme forms, flavin mononucleotide and flavin adenine dinucleotide, is essential for multiple redox reactions necessary for energy production, antioxidant protection, and metabolism of other B vitamins, such as niacin, pyridoxine, and folate. Erythrocyte glutathione reductase activity coefficient (EGRac) is a biomarker of riboflavin status; ratios ≥1.40 are commonly interpreted as indicating biochemical deficiency. Most research on riboflavin status comes from low-income countries and rural settings, which reported high rates of riboflavin deficiency and inadequate intake. However, some studies suggest that riboflavin deficiency, based on the functional indicator EGRac, is also of concern in middle- and high-income countries. Biochemical riboflavin deficiency that does not cause clinical symptoms may contribute to anemia, particularly among women and children. Riboflavin enhances iron absorption, and riboflavin deficiency decreases iron mobilization from stores. The current knowledge on riboflavin’s role in metabolic processes and its biochemical status is summarized in this review, and the available evidence on the role of riboflavin in anemia among different populations is discussed.