bluuebunny/crossref_metadata_2025_split huggingface dataset:
Managing insect and plant pathogen pests with organic and conventional pesticides in onions
Authors: Constancio Natalie , Higgins Douglas , Hausbeck Mary , Szendrei Zsofia 
Published: November 2023

Abstract
Onion thrips (Thrips tabaci Lindeman, Thysanoptera: Thripidae) is a significant insect pest of onions (Allium cepa L., Asparagales: Amaryllidaceae). In addition to feeding on onion foliage, they may spread plant pathogens. Currently, onion thrips and pathogens are managed as separate pests with insecticides and fungicides. It may be beneficial to manage these pests simultaneously as limiting onion thrips may reduce pathogen damage. We tested combinations of bio- and conventional pesticides in a season-long management program in Michigan onion fields. From 2020 to 2022, we counted onion thrips weekly and visually estimated plant foliage necrotic damage (%) in experimental plots each year. In 2020, we tested 6 treatment programs including: azadirachtin, spinosad, a copper-based fungicide, azadirachtin + copper-based fungicide, spinosad + copper-based fungicide, and untreated control. The thrips populations were not significantly reduced compared to the control, but necrotic damage was reduced significantly in spinosad-treated plots. In 2021, we tested a combination of 8 bio- and conventional pesticide programs. Compared to the control, the bioinsecticides did not reduce onion thrips populations, but the conventional pesticide programs reduced both onion thrips numbers and necrotic damage. In 2022, we tested only conventional insecticide programs but included 3 different action thresholds for initiation and applied them with or without a fungicide, for 8 treatments. All insecticide programs reduced onion thrips compared to the control, the action threshold did not impact thrips numbers significantly. Overall, the use of action thresholds can lead to fewer insecticide applications and a lower incidence of leaf damage.
Between science and art
Authors: Reeve Anna 
Published: November 2023

Abstract
Professor Irene Manton (1904–1988) was in the vanguard of technical advances in botany through the use of electron microscopy. As well as new techniques and discoveries communicated through a considerable body of scientific publications, she left behind a collection of antiquities spanning a broad range of cultures and dates. Through these objects, Manton investigated intellectual problems in the history of science and communicated her findings with a highly original and idiosyncratic approach. At first sight a disparate group of unprovenanced antiquities, through the lens of Manton’s archives this collection can be understood as a rich repository of material evidence. This critical examination of Manton’s collecting practices and the uses she made of her ancient objects provides new evidence for the variety of approaches to collecting and interpreting antiquities, spanning disciplinary boundaries, over the course of the twentieth century.
Political anger, affective injustice, and civic education
Authors: Zembylas Michalinos 
Published: November 2023

Abstract
This article analyses arguments and concerns about the emergence of feelings of anger amongst students, when issues of injustice are encountered in the study of the subject civic education. The aim is to determine the extent to which such concerns supply grounds for regulating anger as counterproductive. In particular, it is argued that to encourage students to forgo all feelings of anger that might be aroused by issues of injustice that students have encountered in civic education—in the name of positive psychology and students’ well-being—not only constitutes a form of ‘affective injustice’, but also unfairly asks students to engage in harmful emotion regulation that reproduces existing exclusions. A crucial task for civic education is to provide learning spaces in which teachers and students can explore the affective complexities of political anger and its consequences.
Theoretical study of inelastic processes in collisions of Y and Y+ with hydrogen atom
Authors: Wang Y , Alexeeva S , Wang F , Liu L , Wu Y , Wang J G , Zhao G , Yakovleva S A , Belyaev A K 
Published: November 2023

ABSTRACT
Utilizing a simplified quantum model approach, the low-energy inelastic collision processes between yttrium atoms (ions) and hydrogen atoms have been studied. Rate coefficients corresponding to the mutual neutralization, ion-pair formation, excitation, and de-excitation processes for the above collision systems have been provided in the temperature range of 1000–10 000 K. Three ionic states and 73 covalent states are considered in calculations for the collisions of yttrium atoms with hydrogen atoms, which include six molecular symmetries and 4074 partial inelastic reaction processes. For the collisions of yttrium ions with hydrogen atoms, one ionic state and 116 covalent states are included, which are related to three molecular symmetries and 13 572 partial inelastic collision processes. It is found that the rate coefficients for the mutual neutralization process have a maximum at T = 6000 K, which is an order of magnitude higher than those of other processes. Notably, the positions of optimal windows for the collisions of yttrium atoms and ions with hydrogen atoms are found near electronic binding energy −2 eV (Y) and −4.4 eV (Y+), respectively. The scattering channels located in or near these optimal windows have intermediate-to-large rate coefficients (greater than 10−12 cm3 s−1). The reported data should be useful in the study of non-local thermodynamic equilibrium modelling.
On the existence of a tight planar relation between stellar specific angular momentum, mass, and effective surface brightness for ALFALFA galaxies
Authors: Elson E 
Published: November 2023

ABSTRACT
Measurements of the dependence of stellar specific angular momentum (j*) on stellar mass (M*) are presented for large samples of galaxies from the Arecibo Legacy Fast ALFA (ALFALFA) survey, spanning the stellar mass range ∼108–1011 M⊙. Accurate estimates of j* are generated using measurements of I-band effective radius and velocity width of the H i line profile. While the full sample (N = 3607) of galaxies yields a j*–M* relation with power-law index α = 0.404 ± 0.03, it is shown that various subsamples have indices that are very similar to the best literature results, yet with comparatively lower intrinsic scatters. A galaxy’s mean I-band surface brightness within its effective radius (&lt;μeff&gt;) is shown to significantly correlate with j*–M* scatter. A 3D plane fit to all N = 3607 galaxies in log10j*–log10M*–&lt;μeff&gt; space yields j* ∝ M0.589 ± 0.002 &lt;μeff&gt;0.193 ± 0.002 with scatter σ = 0.089 dex. &lt;μeff&gt;-selected subsamples of size up to N = 1450 yield power-law j*–M* relations mostly consistent with α = 0.55 ± 0.02 from the literature and with intrinsic scatter ranging from 0.083 to 0.129 dex. Thus, this paper presents new, highly accurate measurements of the j*–M* relation that can be used to better understand the important roles played by angular momentum in the formation and evolution of galaxies.
Modelling solar coronal magnetic fields with physics-informed neural networks
Authors: Baty H , Vigon V 
Published: November 2023

ABSTRACT
We present a novel numerical approach aiming at computing equilibria and dynamics structures of magnetized plasmas in coronal environments. A technique based on the use of neural networks that integrates the partial differential equations of the model, and called physics-informed neural networks (PINNs), is introduced. The functionality of PINNs is explored via calculation of different magnetohydrodynamic (MHD) equilibrium configurations, and also obtention of exact two-dimensional steady-state magnetic reconnection solutions. Advantages and drawbacks of PINNs compared to traditional numerical codes are discussed in order to propose future improvements. Interestingly, PINNs is a meshfree method in which the obtained solution and associated different order derivatives are quasi-instantaneously generated at any point of the spatial domain. We believe that our results can help to pave the way for future developments of time dependent MHD codes based on PINNs.
Evolutionary “Crowdsourcing”: Alignment of Fitness Landscapes Allows for Cross-species Adaptation of a Horizontally Transferred Gene
Authors: Kosterlitz Olivia , Grassi Nathan , Werner Bailey , McGee Ryan Seamus , Top Eva M , Kerr Benjamin 
Published: November 2023

Abstract
Genes that undergo horizontal gene transfer (HGT) evolve in different genomic backgrounds. Despite the ubiquity of cross-species HGT, the effects of switching hosts on gene evolution remains understudied. Here, we present a framework to examine the evolutionary consequences of host-switching and apply this framework to an antibiotic resistance gene commonly found on conjugative plasmids. Specifically, we determined the adaptive landscape of this gene for a small set of mutationally connected genotypes in 3 enteric species. We uncovered that the landscape topographies were largely aligned with minimal host-dependent mutational effects. By simulating gene evolution over the experimentally gauged landscapes, we found that the adaptive evolution of the mobile gene in one species translated to adaptation in another. By simulating gene evolution over artificial landscapes, we found that sufficient alignment between landscapes ensures such “adaptive equivalency” across species. Thus, given adequate landscape alignment within a bacterial community, vehicles of HGT such as plasmids may enable a distributed form of genetic evolution across community members, where species can “crowdsource” adaptation.
Elevated MSH2 MSH3 expression interferes with DNA metabolism in vivo
Authors: Medina-Rivera Melisa , Phelps Samantha , Sridharan Madhumita , Becker Jordan , Lamb Natalie A , Kumar Charanya , Sutton Mark D , Bielinsky Anja , Balakrishnan Lata , Surtees Jennifer A 
Published: November 2023

Abstract
The Msh2–Msh3 mismatch repair (MMR) complex in Saccharomyces cerevisiae recognizes and directs repair of insertion/deletion loops (IDLs) up to ∼17 nucleotides. Msh2–Msh3 also recognizes and binds distinct looped and branched DNA structures with varying affinities, thereby contributing to genome stability outside post-replicative MMR through homologous recombination, double-strand break repair (DSBR) and the DNA damage response. In contrast, Msh2–Msh3 promotes genome instability through trinucleotide repeat (TNR) expansions, presumably by binding structures that form from single-stranded (ss) TNR sequences. We previously demonstrated that Msh2–Msh3 binding to 5′ ssDNA flap structures interfered with Rad27 (Fen1 in humans)-mediated Okazaki fragment maturation (OFM) in vitro. Here we demonstrate that elevated Msh2–Msh3 levels interfere with DNA replication and base excision repair in vivo. Elevated Msh2–Msh3 also induced a cell cycle arrest that was dependent on RAD9 and ELG1 and led to PCNA modification. These phenotypes also required Msh2–Msh3 ATPase activity and downstream MMR proteins, indicating an active mechanism that is not simply a result of Msh2–Msh3 DNA-binding activity. This study provides new mechanistic details regarding how excess Msh2–Msh3 can disrupt DNA replication and repair and highlights the role of Msh2–Msh3 protein abundance in Msh2–Msh3-mediated genomic instability.
RVdb: a comprehensive resource and analysis platform for rhinovirus research
Authors: Zhao Peng , Zhou Siyu , Xu Panpan , Su Haoxiang , Han Yelin , Dong Jie , Sui Hongtao , Li Xin , Hu Yongfeng , Wu Zhiqiang , Liu Bo , Zhang Ting , Yang Fan 
Published: November 2023

Abstract
Rhinovirus (RV), a prominent causative agent of both upper and lower respiratory diseases, ranks among the most prevalent human respiratory viruses. RV infections are associated with various illnesses, including colds, asthma exacerbations, croup and pneumonia, imposing significant and extended societal burdens. Characterized by a high mutation rate and genomic diversity, RV displays a diverse serological landscape, encompassing a total of 174 serotypes identified to date. Understanding RV genetic diversity is crucial for epidemiological surveillance and investigation of respiratory diseases. This study introduces a comprehensive and high-quality RV data resource, designated RVdb (http://rvdb.mgc.ac.cn), covering 26 909 currently identified RV strains, along with RV-related sequences, 3D protein structures and publications. Furthermore, this resource features a suite of web-based utilities optimized for easy browsing and searching, as well as automatic sequence annotation, multiple sequence alignment (MSA), phylogenetic tree construction, RVdb BLAST and a serotyping pipeline. Equipped with a user-friendly interface and integrated online bioinformatics tools, RVdb provides a convenient and powerful platform on which to analyse the genetic characteristics of RVs. Additionally, RVdb also supports the efforts of virologists and epidemiologists to monitor and trace both existing and emerging RV-related infectious conditions in a public health context.
ATR phosphorylates DHX9 at serine 321 to suppress R-loop accumulation upon genotoxic stress
Authors: Liu Mei-Yin , Lin Keng-Ru , Chien Yuh-Ling , Yang Bing-Ze , Tsui Li-Yu , Chu Hsueh-Ping Catherine , Wu Ching-Shyi Peter 
Published: November 2023

Abstract
Aberrant DNA/RNA hybrids (R-loops) formed during transcription and replication disturbances pose threats to genome stability. DHX9 is an RNA helicase involved in R-loop resolution, but how DHX9 is regulated in response to genotoxic stress remains unclear. Here we report that DHX9 is phosphorylated at S321 and S688, with S321 phosphorylation primarily induced by ATR after DNA damage. Phosphorylation of DHX9 at S321 promotes its interaction with γH2AX, BRCA1 and RPA, and is required for its association with R-loops under genotoxic stress. Inhibition of ATR or expression of the non-phosphorylatable DHX9S321A prevents DHX9 from interacting with RPA and R-loops, leading to the accumulation of stress-induced R-loops. Furthermore, depletion of RPA reduces the association between DHX9 and γH2AX, and in vitro binding analysis confirms a direct interaction between DHX9 and RPA. Notably, cells with the non-phosphorylatable DHX9S321A variant exhibit hypersensitivity to genotoxic stress, while those expressing the phosphomimetic DHX9S321D variant prevent R-loop accumulation and display resistance to DNA damage agents. In summary, we uncover a new mechanism by which ATR directly regulates DHX9 through phosphorylation to eliminate stress-induced R-loops.
Direct image to subtype prediction for brain tumors using deep learning
Authors: Hewitt Katherine J , Löffler Chiara M L , Muti Hannah Sophie , Berghoff Anna Sophie , Eisenlöffel Christian , van Treeck Marko , Carrero Zunamys I , El Nahhas Omar S M , Veldhuizen Gregory P , Weil Sophie , Saldanha Oliver Lester , Bejan Laura , Millner Thomas O , Brandner Sebastian , Brückmann Sascha , Kather Jakob Nikolas 
Published: November 2023

Abstract

Background
Deep Learning (DL) can predict molecular alterations of solid tumors directly from routine histopathology slides. Since the 2021 update of the World Health Organization (WHO) diagnostic criteria, the classification of brain tumors integrates both histopathological and molecular information. We hypothesize that DL can predict molecular alterations as well as WHO subtyping of brain tumors from hematoxylin and eosin-stained histopathology slides.

Methods
We used weakly supervised DL and applied it to three large cohorts of brain tumor samples, comprising N = 2845 patients.

Results
We found that the key molecular alterations for subtyping, IDH and ATRX, as well as 1p19q codeletion, were predictable from histology with an area under the receiver operating characteristic curve (AUROC) of 0.95, 0.90, and 0.80 in the training cohort, respectively. These findings were upheld in external validation cohorts with AUROCs of 0.90, 0.79, and 0.87 for prediction of IDH, ATRX, and 1p19q codeletion, respectively.

Conclusions
In the future, such DL-based implementations could ease diagnostic workflows, particularly for situations in which advanced molecular testing is not readily available.
Prophetic Poetry
Authors: Gillingham S E 
Published: November 2023

Abstract
Throughout the previous chapter we noted the various ways in which the prophets used the poetry from their culture in order to communicate effectively. In itself this is little different from any adept contemporary preacher using a variety of illustrations in order to capture the imagination of a congregation. Prophets such as Amos and Isaiah borrowed from the proverbial poetry and rhetorical sayings of wisdom; they used secular songs (Isa. 22: 13); they appropriated funeral laments-over nations, if not over individuals (Amos 5; Isa. r4, 23; Ezek. 27, 28, 32); they used love songs to depict the depth of Yahweh’s love for Israel (Hos. 2, 6; Isa. 5; Jer. 3; Isa. 49, 51, 54); they took up oracles of blessing and cursing (Num. 22-4); and they utilized war poetry in order to dramatize the coming judgement on Israel before the other nations (Amos 3, 6, 9; Isa. 5, m, 28; Jer. 4, 5, 6). In addition, the prophets used a good deal of liturgical poetry from the cult, sometimes in short poetic fragments, and at other times in longer, sustained verse.
The Psalms as Poems (I)
Authors: Gillingham S E 
Published: November 2023

Abstract
We have already observed the tension in Hebrew poetry between an adherence to tradition and an expression of originality: this was especially noticeable with regard to the use of metre and parallelism. Nowhere is this tension more evident than in the psalms. In part this is because of their ‘life-centredness’: being responsive as much to experience of life as to liturgical formulas, the psalmists have used conventional forms with a creative freedom.
The Psalter: Hymn-Book, Prayer-Book, or Anthology?
Authors: Gillingham S E 
Published: November 2023

Abstract
A. Looking at the Psalter as a Whole The previous two chapters focused on the psalms as individual poems, with a particular ‘setting-in-life’ or a ‘setting-in-liturgy’- either that of the public Temple liturgy, or the private lives of individuals. They have a different orientation from other Old Testament poems which are more integrated with narrative, and so have a ‘setting-in-literature’.
Local anaesthetic equipment
Authors: Meechan John G , Robb Nigel D , Seymour Robin A 
Published: November 2023

Abstract
The equipment used to deliver local anaesthetic solutions comprises three components. These are the needle, the dental local anaesthetic cartridge and the syringe. Needles consist of a shank and a hub (Fig. 4.1). The end which penetrates the mucosa has a bevel, the part which enters the local anaesthetic cartridge is normally butt-ended. Most needles have one exit point in the bevel although some designs have two. The shank of the needle is made from stainless steel and the hub from stainless steel or plastic.
Local anaesthesia in the maxilla
Authors: Meechan John G , Robb Nigel D , Seymour Robin A 
Published: November 2023

Abstract
Local anaesthesia in the maxilla relies mainly on infiltration techniques (see Chapter 6). This is because the roots of the maxillary teeth are separated from the soft tissues on the buccal aspect by bone that has a fine cortical plate. The thin buccal cortical plate does not represent a barrier to the diffusion of local anaesthetic solution.
Intraligamentary, i.ntraosseous, and intrapulpal anaesthesia
Authors: Meechan John G , Robb Nigel D , Seymour Robin A 
Published: November 2023

Abstract
The previous two chapters have considered the conventional approaches to dental local anaesthesia. In this chapter other techniques are discussed. These are generally regarded as supplementary methods and are often used when conventional means fail. However, many practitioners will use the approaches described below as first-choice techniques for some treatments.
Local anaesthesia: contra-indications and complications
Authors: Meechan John G , Robb Nigel D , Seymour Robin A 
Published: November 2023

Abstract
No drug is without unwanted effects and most therapeutic agents cannot be used with the same degree of safety in all individuals. This chapter considers the contra-indications and adverse effects of dental local anaesthesia. Although the list of complications in this chapter is long it must be stressed that the use of local anaesthetics in dentistry is extremely safe. Indeed, major complications are so rare they are newsworthy.
Non-pharmacological methods of pain control
Authors: Meechan John G , Robb Nigel D , Seymour Robin A 
Published: November 2023

Abstract
This chapter considers the use of mechanisms of pain and anxiety control which do not rely upon the administration of drugs. However, the term ‘non pharmacological’ is not strictly accurate as the mechanism of action of some of these methods relies upon the release of endogenous chemicals such as opioids. This can be defined as an altered state of mind, such that suggestions are accepted more readily, and acted on more powerfully than would be expected in the fully conscious state.
Inhalation sedation
Authors: Meechan John G , Robb Nigel D , Seymour Robin A 
Published: November 2023

Abstract
Inhalation sedation is a technique which has gone through phases of relative popularity, as well as periods of great neglect in the dental profession. It has been dismissed as being too expensive and ineffective. Despite these criticisms the technique continues to be taught, and to attract rave reviews from its supporters!! Inhalation sedation has been called by a number of terms. These include ‘relative analgesia’, ‘inhalational psychosedation’, or ‘nitrous oxide/oxygen sedation’. Previously, the terms have been used to describe variations on the theme of inhalation sedation, but are now used interchangeably.
Polypharmacy sedation in dentistry
Authors: Meechan John G , Robb Nigel D , Seymour Robin A 
Published: November 2023

Abstract
Polypharmacy sedation can be defined as the use of more than one central nervous system depressant drug to induce the sedated state and allow treatment to proceed. Usually all of the agents concerned are given intravenously. The use of multiple agents to produce sedation for dental treatment is a con troversial subject. Advocates of this type of sedation are vigorous in its defence, arguing that the quality of sedation produced by multiple agents is significantly better than that produced by a single drug. Those who argue against such tech niques maintain that the synergistic actions of the drugs which enhance the sedation, also increase unwanted side effects, such as respiratory depression. The synergistic rise in side effects, most notably respiratory depression, make the tech niques too dangerous to be used under any circumstances.
Medicolegal aspects of the practice of sedation in dentistry
Authors: Meechan John G , Robb Nigel D , Seymour Robin A 
Published: November 2023

Abstract
It is important that those who practise dentistry are aware of the potential medicolegal pitfalls in their practice. This chapter will concentrate on the medicolegal aspects of the practice of sedation. In addition, it must be remem bered that as well as the issues surrounding the practice of sedation, the standards of dental care must be maintained to avoid the potential problems that could occur from that source.