bluuebunny/crossref_metadata_2025_split huggingface dataset:
Susceptibilities of Helicoverpa zea (Lepidoptera: Noctuidae) Populations From the Mississippi Delta to a Diamide Insecticide
Authors: Allen K C , Little N S , Perera O P 
Published: November 2022

Abstract
The corn earworm, Helicoverpa zea (Boddie), is a major pest of row crops in the Southern United States. Control of this insect is dependent on preventative insecticidal transgenic crops and synthetic insecticide applications when damaging populations are encountered in the field. Recently, the use of chemicals from the diamide class of insecticides, particularly chlorantraniliprole, has been used to control unacceptable populations. Due to the increased importance of this active ingredient for control of corn earworms, populations of this insect from the Mississippi Delta have been monitored for susceptibilities annually since 2016. Overall, 58 populations of H. zea were examined for their susceptibility to chlorantraniliprole through diet-incorporated bioassays from 2016 to 2021. Based on probit analysis, there was only a 4-fold difference between the highest and lowest LC50 estimates for all populations tested. Through weights of 2nd and 3rd instar larvae, there appears to be a substantial fitness cost associated with surviving caterpillars that fed on various concentrations of chlorantraniliprole in bioassays, which is not captured through the yes or no response of typical survival analysis. Overall, there was not a detectable trend of reduced susceptibility to chlorantraniliprole over the course of the six-year study.
The historic mineralogical instruments collection of the Real Museo Mineralogico, University of Naples Federico II: meaning and value
Authors: Petti Carmela , Cappelletti Piergiulio , Pellino Annamaria 
Published: November 2022

Abstract
The Real Museo Mineralogico of the University of Naples Federico II was established in 1801 by Ferdinando IV of Bourbon and his queen, Maria Carolina. Their aim was to create a centre for minerals research and education. The museum at present preserves over 50,000 objects, mainly minerals, but also books, teaching models and instruments. The last of these form a little-known collection of considerable scientific and historical value. Historical studies of the instruments collection are based on extensive archival research conducted on documents and ancient catalogues of the museum and the Archivio di Stato in Naples. This study describes the main instruments, detailing their date of acquisition, typology and use. Its goal is to provide a testimony to the contribution of the Real Museo Mineralogico to the development of the science of mineralogy in Naples, and at the same time to extend, by means of new data (suppliers, acquisition methods, price), the catalogue of the instruments collection.
Topical Review: Youth With Type 1 Diabetes: What Is the Role of Peer Support?
Authors: Helgeson Vicki S , Berg Cynthia A , Raymaekers Koen 
Published: November 2022

AbstractThe literature on the role of peer support for psychological well-being and disease management among youth with type 1 diabetes (T1D) is mixed. In this topical review, we use self-determination theory (SDT) as a framework to understand the conditions under which peer support is helpful or unhelpful regarding psychological well-being and diabetes management. We briefly review the literature to support our claim that existing research on peer support is inconsistent. A primary reason for the inconsistency is that previous work largely focuses on diabetes instrumental and informational support from peers, which have the potential to threaten SDT needs for autonomy, competence, and relatedness. Instrumental and informational support may set youth with T1D apart from peers at a time when fitting in with peers is crucial. Instead, we argue that emotional support from and companionship with peers best meet the SDT need of relatedness while not posing direct threats to autonomy or competence. We also note that some youth have extremely high needs for relatedness such that they prioritize connecting with peers over diabetes management. We conclude by calling for more research to adopt a SDT theory approach to examine the role of peer support in the lives of youth with T1D and for health care professionals to expand their focus from the specifics of diabetes to the broader social context.
The secreted immune response peptide 1 functions as a phytocytokine in rice immunity
Authors: Wang Pingyu , Jia Huimin , Guo Ting , Zhang Yuanyuan , Wang Wanqing , Nishimura Hideki , Li Zhengguo , Kawano Yoji 
Published: November 2022

AbstractSmall signalling peptides play important roles in various plant processes, but information regarding their involvement in plant immunity is limited. We previously identified a novel small secreted protein in rice, called immune response peptide 1 (IRP1). Here, we studied the function of IRP1 in rice immunity. Rice plants overexpressing IRP1 enhanced resistance to the virulent rice blast fungus. Application of synthetic IRP1 to rice suspension cells triggered the expression of IRP1 itself and the defence gene phenylalanine ammonia-lyase 1 (PAL1). RNA-seq results revealed that 84% of genes up-regulated by IRP1, including 13 OsWRKY transcription factors, were also induced by a microbe-associated molecular pattern (MAMP), chitin, indicating that IRP1 and chitin share a similar signalling pathway. Co-treatment with chitin and IRP1 elevated the expression level of PAL1 and OsWRKYs in an additive manner. The increased chitin concentration arrested the induction of IRP1 and PAL1 expression by IRP1, but did not affect IRP1-triggered mitogen-activated protein kinases (MAPKs) activation. Collectively, our findings indicate that IRP1 functions as a phytocytokine in rice immunity regulating MAPKs and OsWRKYs that can amplify chitin and other signalling pathways, and provide new insights into how MAMPs and phytocytokines cooperatively regulate rice immunity.
White dwarf binaries suggest a common envelope efficiency α ∼ 1/3
Authors: Scherbak Peter , Fuller Jim 
Published: November 2022

ABSTRACT
Common envelope (CE) evolution, which is crucial in creating short-period binaries and associated astrophysical events, can be constrained by reverse modelling of such binaries’ formation histories. Through analysis of a sample of well-constrained white dwarf (WD) binaries with low-mass primaries (seven eclipsing double WDs, two non-eclipsing double WDs, one WD-brown dwarf), we estimate the CE energy efficiency αCE needed to unbind the hydrogen envelope. We use grids of He- and CO-core WD models to determine the masses and cooling ages that match each primary WD’s radius and temperature. Assuming gravitational wave-driven orbital decay, we then calculate the associated ranges in post-CE orbital period. By mapping WD models to a grid of red giant progenitor stars, we determine the total envelope binding energies and possible orbital periods at the point CE evolution is initiated, thereby constraining αCE. Assuming He-core WDs with progenitors of 0.9–2.0 M⊙, we find αCE ∼ 0.2–0.4 is consistent with each system we model. Significantly higher values of αCE are required for higher mass progenitors and for CO-core WDs, so these scenarios are deemed unlikely. Our values are mostly consistent with previous studies of post-CE WD binaries, and they suggest a nearly constant and low envelope ejection efficiency for CE events that produce He-core WDs.
The volumetric extended-Schmidt law: a unity slope
Authors: Du Kaiyi , Shi Yong , Zhang Zhi-Yu , Gu Qiusheng , Wang Tao , Wang Junzhi , Li Xin , Zhai Sai 
Published: November 2022

ABSTRACT
We investigate the extended-Schmidt (ES) law in volume densities (ρSFR ∝ $(\rho _{\rm gas}\rho _{\rm star}^{0.5})^{\alpha ^{\rm VES}}$) for spatially resolved regions in spiral, dwarf, and ultra-diffuse galaxies (UDGs), and compare to the volumetric Kennicutt–Schmidt (KS) law (ρSFR ∝ $\rho _{\rm gas}^{\alpha ^{\rm VKS}}$). We first characterize these star formation laws in individual galaxies using a sample of 11 spirals, finding median slopes αVES = 0.98 and αVKS = 1.42, with a galaxy-to-galaxy rms fluctuation that is substantially smaller for the volumetric ES law (0.18 versus 0.41). By combining all regions in spirals with those in additional 13 dwarfs and one UDG into one single data set, it is found that the rms scatter of the volumetric ES law at given x-axis is 0.25 dex, which is also smaller than that of the volumetric KS law (0.34 dex). At the extremely low gas density regime as offered by the UDG, the volumetric KS law breaks down but the volumetric ES law still holds. On the other hand, as compared to the surface density ES law, the volumetric ES law instead has a slightly larger rms scatter, consistent with the scenario that the ES law has an intrinsic slope of αVES ≡1 but the additional observational error of the scale height increases the uncertainty of the volume density. The unity slope of the ES law implies that the star formation efficiency (= ρSFR/ρgas) is regulated by the quantity that is related to the $\rho _{\rm star}^{0.5}$.
Field-based physical inference from peculiar velocity tracers
Authors: Prideaux-Ghee James , Leclercq Florent , Lavaux Guilhem , Heavens Alan , Jasche Jens 
Published: November 2022

ABSTRACT
We present a proof-of-concept Bayesian hierarchical modelling approach to reconstruct the initial cosmic matter density field constrained by peculiar velocity observations. Using a model for the gravitational evolution of dark matter to connect the initial conditions to late-time observations, it reconstructs the late-time density and velocity fields as natural byproducts. We implement this field-based physical inference approach by adapting the Bayesian Origin Reconstruction from Galaxies ($\small {\rm BORG}$) algorithm, which explores the high-dimensional posterior through the use of Hamiltonian Monte Carlo sampling. We test the self-consistency of the method using random sets of tracers, and assess its accuracy in a more complex scenario where peculiar velocity tracers are mock haloes drawn from $\small {\rm GADGET2}$ N-body simulations. We find that our framework self-consistently infers the initial conditions, density and velocity fields, and shows some robustness to model mis-specification. Compared with the approach of constrained Gaussian random fields/Wiener filtering, the hierarchical model produces more accurate final density and velocity field reconstructions. It also allows us to constrain the initial conditions by peculiar velocity observations, complementing in this aspect other field-based approaches based on alternative cosmological observables such as galaxy clustering or weak lensing.
Engineered multiple translation initiation sites: a novel tool to enhance protein production in Bacillus licheniformis and other industrially relevant bacteria
Authors: Zhang Manyu , Song Jing , Xiao Jun , Jin Jingjie , Nomura Christopher T , Chen Shouwen , Wang Qin 
Published: November 2022

Abstract
Gram-positive bacteria are a nascent platform for synthetic biology and metabolic engineering that can provide new opportunities for the production of biomolecules. However, the lack of standardized methods and genetic parts is a major obstacle towards attaining the acceptance and widespread use of Gram-positive bacterial chassis for industrial bioproduction. In this study, we have engineered a novel mRNA leader sequence containing more than one ribosomal binding site (RBS) which could initiate translation from multiple sites, vastly enhancing the translation efficiency of the Gram-positive industrial strain Bacillus licheniformis. This is the first report elucidating the impact of more than one RBS to initiate translation and enhance protein output in B. licheniformis. We also explored the application of more than one RBS for both intracellular and extracellular protein production in B. licheniformis to demonstrate its efficiency, consistency and potential for biotechnological applications. Moreover, we applied these concepts for use in other industrially relevant Gram-positive bacteria, such as Bacillus subtilis and Corynebacterium glutamicum. In all, a highly efficient and robust broad-host expression element has been designed to strengthen and fine-tune the protein outputs for the use of bioproduction in microbial cell factories.
Interactions of small molecules with DNA junctions
Authors: McQuaid Kane T , Pipier Angélique , Cardin Christine J , Monchaud David 
Published: November 2022

Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing
Authors: Bonin Nathalie , Doster Enrique , Worley Hannah , Pinnell Lee J , Bravo Jonathan E , Ferm Peter , Marini Simone , Prosperi Mattia , Noyes Noelle , Morley Paul S , Boucher Christina 
Published: November 2022

Abstract
Antimicrobial resistance (AMR) is considered a critical threat to public health, and genomic/metagenomic investigations featuring high-throughput analysis of sequence data are increasingly common and important. We previously introduced MEGARes, a comprehensive AMR database with an acyclic hierarchical annotation structure that facilitates high-throughput computational analysis, as well as AMR++, a customized bioinformatic pipeline specifically designed to use MEGARes in high-throughput analysis for characterizing AMR genes (ARGs) in metagenomic sequence data. Here, we present MEGARes v3.0, a comprehensive database of published ARG sequences for antimicrobial drugs, biocides, and metals, and AMR++ v3.0, an update to our customized bioinformatic pipeline for high-throughput analysis of metagenomic data (available at MEGLab.org). Database annotations have been expanded to include information regarding specific genomic locations for single-nucleotide polymorphisms (SNPs) and insertions and/or deletions (indels) when required by specific ARGs for resistance expression, and the updated AMR++ pipeline uses this information to check for presence of resistance-conferring genetic variants in metagenomic sequenced reads. This new information encompasses 337 ARGs, whose resistance-conferring variants could not previously be confirmed in such a manner. In MEGARes 3.0, the nodes of the acyclic hierarchical ontology include 4 antimicrobial compound types, 59 resistance classes, 233 mechanisms and 1448 gene groups that classify the 8733 accessions.
The IMG/M data management and analysis system v.7: content updates and new features
Authors: Chen I-Min A , Chu Ken , Palaniappan Krishnaveni , Ratner Anna , Huang Jinghua , Huntemann Marcel , Hajek Patrick , Ritter Stephan J , Webb Cody , Wu Dongying , Varghese Neha J , Reddy T B K , Mukherjee Supratim , Ovchinnikova Galina , Nolan Matt , Seshadri Rekha , Roux Simon , Visel Axel , Woyke Tanja , Eloe-Fadrosh Emiley A , Kyrpides Nikos C , Ivanova Natalia N 
Published: November 2022

AbstractThe Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. We also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).
High-entropy metal oxide containing hybrid electrolyte for long-life Li-metal batteries
Authors: Li Mingsheng , Wang Liqi , Shi Yongzheng , Zhang Jikai , Zhu Qi , Shang Jiaxiang , Li Bin , Yang Shubin 
Published: November 2022

AbstractSolid-state electrolytes are responsible for transporting lithium (Li) ions between electrodes in solid-state batteries and are essential for high-safety and high-energy Li-metal batteries. Developing novel solid-state electrolytes with high ionic conductivity and good interfacial contact is an urgent need. Here, to this end, a solid-state hybrid electrolyte is developed by mixing high-entropy Li-containing metal oxide (Lix(Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)1−xO, HEOLi) matrix and poly(ethylene oxide)–Li salt binder and casting on polytetrafluoroethylene (PTFE) substrate. By virtue of the low Li-ion migration energy barrier of the HEOLi (0.36 eV) and the strong interaction between the oxygen vacancies of the HEOLi and the Li salt anions, a biphasic transport of Li ions in both inorganic and polymeric phases of the hybrid electrolyte is achieved, yielding a high ionic conductivity of 3 × 10−4 S cm−1 at 30°C. The Li/Li symmetric cells with the hybrid electrolyte show a low overpotential of 45 mV and a long cycle life of more than 2500 h. Furthermore, coupled with the LiFePO4 cathodes and metallic Li anodes, solid-state full cells with the hybrid electrolyte deliver a high capacity of 150 mAh g−1, stable cycle performance and high safety. Consequently, hybrid electrolytes based on high-entropy metal oxides have broad application prospects in solid-state electrochemical energy storage and are expected to achieve Li-metal batteries with high-safety, high-energy density and long life.
Ice plant root plasma membrane aquaporins are regulated by clathrin-coated vesicles in response to salt stress
Authors: Gómez-Méndez María Fernanda , Amezcua-Romero Julio César , Rosas-Santiago Paul , Hernández-Domínguez Eric Edmundo , de Luna-Valdez Luis Alberto , Ruiz-Salas Jorge Luis , Vera-Estrella Rosario , Pantoja Omar 
Published: November 2022

Abstract
The regulation of root Plasma membrane (PM) Intrinsic Protein (PIP)-type aquaporins (AQPs) is potentially important for salinity tolerance. However, the molecular and cellular details underlying this process in halophytes remain unclear. Using free-flow electrophoresis and label-free proteomics, we report that the increased abundance of PIPs at the PM of the halophyte ice plant (Mesembryanthemum crystallinum L.) roots under salinity conditions is regulated by clathrin-coated vesicles (CCV). To understand this regulation, we analyzed several components of the M. crystallinum CCV complexes: clathrin light chain (McCLC) and subunits μ1 and μ2 of the adaptor protein (AP) complex (McAP1μ and McAP2μ). Co-localization analyses revealed the association between McPIP1;4 and McAP2μ and between McPIP2;1 and McAP1μ, observations corroborated by mbSUS assays, suggesting that AQP abundance at the PM is under the control of CCV. The ability of McPIP1;4 and McPIP2;1 to form homo- and hetero-oligomers was tested and confirmed, as well as their activity as water channels. Also, we found increased phosphorylation of McPIP2;1 only at the PM in response to salt stress. Our results indicate root PIPs from halophytes might be regulated through CCV trafficking and phosphorylation, impacting their localization, transport activity, and abundance under salinity conditions.
Methotrexate, leflunomide and tacrolimus use and the progression of rheumatoid arthritis-associated interstitial lung disease
Authors: Kim Ji-Won , Chung Sang Wan , Pyo Jung Yoon , Chang Sung Hae , Kim Min Uk , Park Chan Ho , Lee Ji Sung , Lee Jeong Seok , Ha You-Jung , Kang Eun Ha , Lee Yeon-Ah , Park Yong-Beom , Lee Eun Young , Choe Jung-Yoon 
Published: November 2022

Abstract

Objective
To examine the association between MTX, LEF and tacrolimus use and the progression of RA-associated interstitial lung disease (ILD).

Methods
The Korean RA-ILD cohort prospectively enrolled patients with RA-associated ILD at multiple centres from 2015 to 2018 and followed up with them for 3 years. ILD progression was defined by any of the followings: a decrease of ≥10% in forced vital capacity, a decrease of ≥15% in the diffusing capacity of the lung for carbon monoxide, or death from respiratory failure.

Results
Of 143 patients, 64 patients experienced ILD progression during a median follow-up period of 33 months. The use of MTX [adjusted hazard ratio (aHR), 1.06; 95% CI, 0.59, 1.89], LEF (aHR, 1.75; 95% CI, 0.88, 3.46) and tacrolimus (aHR, 0.94; 95% CI, 0.52, 1.72) did not increase the risk of ILD progression. However, the association between LEF use and the risk of ILD progression was significant in subgroups with poor lung function (aHR, 8.42; 95% CI, 2.61, 27.15). Older age, male sex, a shorter RA duration, higher RA disease activity and extensive disease at baseline were independently associated with ILD progression.

Conclusion
None of the three treatments increased the risk of RA-associated ILD progression, except for LEF, which increased the risk of ILD progression in patients with severe ILD. The appropriate use of conventional synthetic disease-modifying antirheumatic drugs considering RA disease activity and ILD severity would be important for the management of RA-associated ILD.
Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process
Authors: Barido-Sottani Joëlle , Żyła Dagmara , Heath Tracy A 
Published: November 2022

Abstract
Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical data sets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical data set of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical data sets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits. [Bayesian phylogenetic inference; fossil age estimates; fossilized birth-death; Lagerstätte; total-evidence.]