bluuebunny/crossref_metadata_2025 huggingface dataset:
Ubiquitous genome streamlined Acidobacteriota in freshwater environments
Authors: Wong Hon Lun , Bulzu Paul-Adrian , Ghai Rohit , Chiriac Maria-Cecilia , Salcher Michaela M
Published: October 2024

Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K2, cbb3-type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus, with two new species named “A. lacustris” and “A. fluvialis”. Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments.
Inoculum effect of cefiderocol against NDM-1 producing Escherichia coli in vitro and in a murine model of peritonitis
Authors: Godron Anne-Sophie , Amoura Ariane , Pistien Claire , Birgy André , Magreault Sophie , Jousset Agnès B , Jullien Vincent , Lefort Agnès , Fantin Bruno , El Meouche Imane , de Lastours Victoire
Published: October 2024

Introduction

Cefiderocol is a siderophore cephalosporin active in vitro against carbapenemase-producing Enterobacterales, including New Delhi metallo-β-lactamases (NDM-1). A significant impact of the size of bacterial inoculum on its efficacy has been described in vitro, the clinical impact of which is unclear. Here, we analyse the inoculum effect of cefiderocol against E. coli-NDM-1 in vitro and in a murine peritonitis model.

Materials and Methods

Escherichia coli 62-pTOPO and its isogenic variant expressing NDM-1, 62-pTOPO-NDM, were constructed from a clinical strain. MICs and bactericidal kinetics were determined at standard (105 cfu/mL) and high inoculum (107 cfu/mL). The in vivo effect was assessed in a severe murine peritonitis model, comparing low (106 cfu/mL) and high (108 cfu/mL) inoculum. Survival rates, organ sterilization and bacterial counts in spleen and peritoneal fluid were compared.

Results

Cefiderocol MICs for 62-pTOPO and 62-pTOPO-NDM at standard and high inoculum were 0.008, 2, 2 and 1024 mg/L, respectively. Bactericidal activity was not achieved in vitro for 62-pTOPO-NDM at high inoculum with high cefiderocol concentrations (16 mg/L). In vivo, for 62-pTOPO-NDM, no difference was found in survival, organ sterilization or bacterial counts between low and high inoculum. For 62-pTOPO, no difference was observed in survival, despite less organ sterilization and higher bacterial counts in organs with the high inoculum.

Conclusion

A significant inoculum effect of cefiderocol was observed in vitro for 62-pTOPO and 62-pTOPO-NDM. However, the effectiveness of cefiderocol was not reduced in vivo with a high bacterial inoculum. In vitro inoculum effect of cefiderocol may not be clinically significant.
Emergent resistance-associated mutations at first- or second-line HIV-1 virologic failure with second-generation InSTIs in two- and three-drug regimens: the Virostar-1 study
Authors: Marcelin Anne-Geneviève , Soulie Cathia , Wirden Marc , Barriere Guillaume , Durand François , Charpentier Charlotte , Descamps Diane , Calvez Vincent
Published: October 2024

Background

Second-generation integrase strand transfer inhibitors (InSTIs) have a high barrier to resistance and potent antiretroviral activity. They are recommended as first- or second-line (FL and SL) options in two- and three-drug regimens (2DR and 3DR) in international treatment guidelines. However, there are limited real-world data on emerging resistance at the time of virological failure (VF) with these regimens.

Objectives

The Virostar-1 study objective is to analyse the emergence of resistance-associated mutations (RAMs) over 3 years with DTG-based 2DRs and DTG- or bictegravir (BIC)-based 3DRs in people living with HIV (PLWH) experiencing a VF (FL or SL).

Methods

Retrospective analysis of genotypic resistance detected at the time of a FL or SL VF with BIC/FTC/TAF, DTG/ABC/3TC, DTG/3TC and DTG/RPV between 2019 and 2022 was conducted from a French multicentre database. VF was defined as two consecutive HIV-1 plasma viral loads > 50 c/mL. Sanger assays were performed at VF within standard clinical care. Resistance mutations were reported using the ANRS algorithm. Selection biases prevent group comparisons.

Results

During the period, N = 5986 PLWH were followed either in FL or SL. The VF rate was overall low: BIC/FTC/TAF, 6.8%; DTG/ABC/3TC, 7.5%; DTG/3TC, 5.1%; and DTG/RPV, 2.1%. Some emergent InSTI or NRTI RAMs were detected with BIC/FTC/TAF 4%, DTG/ABC/3TC 8.5%, DTG/3TC 18% and 39% emergent NNRTI RAMs with DTG/RPV. However, a complete absence of dual resistance against NRTIs and InSTIs was observed.

Conclusions

We detected rare emergent InSTI RAMs and few emergent NRTI RAMs in PLWH failing DTG- or BIC-based regimens in FL or SL. The observed rates of emergent RAMs at VF were 4% with BIC/FTC/TAF, 8.5% with DTG/ABC/3TC, 18% with DTG/3TC and 39% with DTG/RPV.
Identifying and modeling the impact of neonicotinoid exposure on honey bee colony profit
Authors: Bixby Miriam , French Sarah K , Wizenberg Sydney B , Jamieson Aidan , Pepinelli Mateus , Cunningham Morgan M , Conflitti Ida M , Foster Leonard J , Zayed Amro , Guarna Maria Marta
Published: October 2024

Pollination by the European honey bee, Apis mellifera, is essential for the production of many crops, including highbush blueberries (Vaccinum corymbosum). To understand the impact of agrochemicals (specifically, neonicotinoids, a class of synthetic, neurotoxic insecticides) on these pollinators, we conducted a field study during the blueberry blooms of 2020 and 2021 in British Columbia (B.C.). Forty experimental honey bee colonies were placed in the Fraser Valley: half of the colonies were located within 1.5 km of highbush blueberry fields (“near” colonies) and half were located more than 1.5 km away (“far” colonies). We calculated risk quotients for these compounds using their chronic lethal dietary dose (LDD50) and median lethal concentration (LC50). Pesticide risk was similar between colonies located near and far from blueberry forage, suggesting that toxicity risks are regionally ubiquitous. Two systemic neonicotinoid insecticides, clothianidin and thiamethoxam, were found at quantities that exceeded chronic international levels of concern. We developed a profit model for a pollinating beekeeper in B.C. that was parameterized by: detected pesticide levels; lethal and sublethal bee health; and economic data. For colonies exposed to neonicotinoid pesticides in and out of the blueberry forage radii, there were economic consequences from colony mortality and sublethal effects such as a loss of honey production and compromised colony health. Further, replacing dead colonies with local bees was more profitable than replacing them with imported packages, illustrating that beekeeping management selection of local options can have a positive effect on overall profit.
Behavioral responses of Araecerus fasciculatus (Coleoptera: Anthribidae) to volatiles of selected stored Chinese medicinal plant products
Authors: Zeng Guang , Xie Songhai , Jian Lingyan , Agrafioti Paraskevi , Wu Kaixian , Athanassiou Christos G , Cao Yu
Published: October 2024

The olfactory responses of Araecerus fasciculatus Degeer to the volatiles of 5 traditional Chinese medicine plant products (CMPPs; i.e., Codonopsis pilosula Franch., Ophiopogon japonicus Linn. f., Astragalus membranaceus Fisch., Dendrobium nobile Lindl., and Angelica dahurica Fisch.) were studied using Y-tube, 4-arm, and 6-arm olfactometers. The volatile components of these CMPPs were analyzed using gas chromatography–mass spectrometry (GC–MS). A. fasciculatus significantly preferred the CMPPs volatiles in the order of O. japonicus > C. pilosula > A. membranaceus ≥ D. nobile = A. dahurica. In the volatile profiles of O. japonicus, C. pilosula, A. membranaceus, D. nobile, and A. dahurica, GC–MS identified 27, 61, 63, 52, and 71 components, respectively, and β-elemene (30.58%), hexanal (12.69%), selina-3,7(11)-diene (12.31%), d-limonene (18.59%), and α-curcumene (8.88%) were the most abundant volatile components. A. fasciculatus were attracted to β-elemene, α-selinene, and β-selinene (main components of the volatile profiles of the most preferred CMPPs of O. japonicus) at different concentrations, with 1, 50, and 25 µg/µl being the most attractive, respectively. The olfactory preferences of A. fasciculatus were β-elemene > α-selinene = β-selinene based on the 4-arm olfactometer bioassays for comparisons at their most attractive concentrations. Therefore, differences in the volatile profiles among CMPPs significantly influenced the olfactory responses of A. fasciculatus, offering insight into the mechanisms of host preferences in stored-product pests based on chemical ecology. β-elemene showed the greatest potential to be developed as an attractant for the monitoring and control of this pest.
Tendency to mate with short-winged partner of the brown planthopper Nilaparvata lugens (Hemiptera: Delphacidae)
Authors: He Yi-Nan , Bu Tong-Lei , Liu Xiang-Dong
Published: October 2024

Wing dimorphism is a distinguishing characteristic of brown planthopper Nilaparvata lugens (Stål) populations, wherein adults exhibit 2 distinct morphs: long-winged and short-winged. The presence of long-winged individuals often heralds the onset of migration, while short-winged morphs signify high reproduction and can be associated with population outbreaks. This phenomenon underscores the adaptability of these insects in response to environmental cues and their impact on agricultural ecosystems. Wing morphs of N. lugens are controlled by genetical and environmental factors. Mate choice between long and short-winged adults affects wing morphs of offspring. In this study, we found that the wild population had no persistent preference for choosing long-winged or short-winged adults to mate. But in 2 multigenerational selected lineages for long and short-winged morphs, the short-winged males preferred to short-winged females to mate and the long-winged males had no preference. In the nearly pure-bred lineages of long-winged and short-winged morphs, both wing morphs of females preferred for short-winged males. Purification of wing morph lineages enhanced mating preference for short-winged partners. When the wing developmental gene InR1 or InR2 was interfered by RNAi, the pure-bred lineage of long-winged morph mainly produced short-winged adults and the short-winged morphs produced long-winged adults, and these adults exhibited preference to mate with short-winged partners. The tendency to mate with short-winged morphs leads to more short-winged offspring which easily causes the rapid growth of populations.
‘We Don’t Have Any Honor Because We Are khwaja sira’: Police Violence and Discrimination Against the Khwaja Sira Community in Swat, Pakistan
Authors: Tripathi Saumya , Azhar Sameena , Ahmad Imtyaz
Published: October 2024

This qualitative study examines police violence and discriminatory policing practices targeting the third gender community, known in Pakistan as khwaja sira. Employing a phenomenological analysis, we conducted a qualitative study involving in-depth interviews with 45 khwaja sira in Mingora, Khyber Pakhtunkhwa, Pakistan, recruited through purposive and snowball sampling. Using Interpretative Phenomenological Analysis of the interview transcripts: two distinct themes emerged regarding the lived experiences of khwaja sira in Swat, Pakistan: experiencing multiple forms of violence by police; and managing abuses of policing power. Findings shed light on the challenges khwaja sira face regarding police violence and misconduct, including neglect from law enforcement officers to register their cases, biased practices within police precincts, and discrimination associated with their engagement in sex work or their gender nonconformity. Findings underscore the need for comprehensive interventions aimed at addressing police violence experienced by the khwaja sira community.
Distinct deregulation trends of transcriptional protein complexes in aging naive T cells
Authors: Kökrek Emel , Pir Pınar
Published: October 2024

The impact of aging on T cell subsets, specifically CD4+ and CD8+ T cells, leading to immune system dysfunction has been the focus of scientific investigation due to its potential to reverse age-associated deterioration. Transcriptomic and epigenomic studies have identified the primary regulators in T cell aging. However, comprehending the underlying dynamic mechanisms requires studying these proteins with their interactors. Here, we integrated single-cell RNA sequencing data of naive CD4+ and CD8+ T cells obtained from 3 different age groups with protein-protein and domain-domain interaction networks to predict and compare the transcriptional protein complexes and identify their capacity to explain age-associated variances. Our novel approach revealed significant effects of aging on the repertoire of complexes, which remains unchanged in naive CD4+ T cells, while in naive CD8+ T cells, it diminishes. In both cell types, there was major deregulation of complexes with the same composition, involving a range of transcription factors. This aging-associated deregulation is characterized by a specific set of protein complexes in naive CD4+ T cells, but this pattern is not observed in naive CD8+ T cells. SMAD3 and BCL11A complexes emerge as key markers in defining a trajectory in aging naive CD4+ T cells. These complexes can accurately distinguish between 3 different age groups, indicating their potential as targets. The direct link between SMAD3 and FOS complexes whose regulatory role has been previously implicated in aging and MBD3 as the novel key link between SMAD3 and BCL11A complexes implicates a coordinated mechanism in age-associated deregulation.
Spatial and temporal partitioning between eastern gray and fox squirrels in a Central Hardwood forest
Authors: Remmers Justin J , Lesmeister Damon B , Nielsen Clayton K
Published: October 2024

Congeneric fox squirrels (Sciurus niger) and eastern gray squirrels (S. carolinensis) compete for resources within North American temperate forests. Both species exhibit regional variation in morphology and behavior—potentially due to differences in geography, community composition, or ecological pressures between forested regions. While many have studied these species in other forested regions of the United States, recent assessments of partitioning between these species in Central Hardwood forests remain scarce. We investigated spatial and temporal partitioning between squirrel species using photographic captures from camera traps at 2 scales (i.e., camera location and camera cluster) across a 16,058-km2 region of southern Illinois, United States, during January to April 2008 to 2010. We fitted single-season single-species and co-occurrence occupancy models to assess spatial partitioning at both scales and used kernel density analysis to assess temporal partitioning. We recorded 3,044 photographic captures of focal species (n = 918 fox squirrels and 2,126 eastern gray squirrels). Fox Squirrel occupancy was 0.26 ± 0.09 (SE) and 0.50 ± 0.17 at the camera location and camera cluster scales, respectively. Eastern Gray Squirrel occupancy was 0.47 ± 0.07 and 0.84 ± 0.23 at the camera location and camera cluster scales, respectively. Fox Squirrel occupancy increased with further distances to roads and had scale-dependent relationships to forest structure. Eastern Gray Squirrel occupancy increased with more hardwood basal area. Co-occurrence was influenced by distance to road at the camera location scale. We found a moderate level of activity overlap between species (Δ = 0.63, CI = 0.60 to 0.67); however, no evidence of temporal partitioning was observed. Habitat characteristics and spatial scale appear more influential in partitioning eastern gray and fox squirrels in Central Hardwood forests than peak activity.
Genetic characterization of immune adaptor molecule MyD88 in Culex pipiens complex (Diptera: Culicidae) mosquitoes from China
Authors: Wang Xueting , Zhu Lilan , Huo Caifei , He Dan , Tian Haifeng , Fan Xiaolan , Lyu Yongqing , Li Yan
Published: October 2024

Mosquitoes of the Culex (Cx.) pipiens complex are vectors of severe diseases including West Nile fever by West Nile virus, Japanese encephalitis by Japanese encephalitis virus, and Lymphatic filariasis by filarial nematode Wuchereria bancrofti. As a major portion of mosquito immune system, the Toll pathway implicates in response against infections of mosquito-borne pathogens and biocontrol agents. The genetic diversity of immune-related molecules is expected to be a feasible and effective introduction to expand our knowledge of the mosquito-microbe interplay. However, a comprehensive description is currently lacking regarding the genetic characteristic of the Toll pathway molecules in Cx. pipiens complex mosquitoes. In the present study, genetic changes in Cx. pipiens complex MyD88 (Myeloid differentiation primary response protein 88) were analyzed as a precedent for the Toll pathway molecules in this taxon. MyD88 is a critical adaptor of the pathway transducing signals from TIR-containing receptors to downstream death domain-containing molecules. Our results revealed that adaptive selection has influenced the genetic changes of the molecule, giving rise to acceleration of diversity at a number of amino acid sites. The adaptively selected sites lie in the death domain, intermediate domain, and C-terminal extension. The characteristics of the genetic changes shed insights into the prominent molecular-level structural basis and the involvement strategy of the adaptor in the arms race against exogenous challenges. This finding would be beneficial for further exploration and deeper understanding of the mosquitoes’ vectorial capacity and facilitating the effectiveness and sustainability of the biocontrol agents.
Dengue-mediated changes in the vectorial capacity of Aedes aegypti (Diptera: Culicidae): manipulation of transmission or infection by-product?
Authors: Mateescu Ioana , Lequime Sebastian
Published: October 2024

An arthropod’s vectorial capacity summarizes its disease transmission potential. Life-history traits, such as fecundity or survival, and behavioral traits, such as locomotor activity, host-seeking and feeding behavior, are important components of vectorial capacity. Studies have shown that mosquito-borne pathogens may alter important vectorial capacity traits of their mosquito vectors, thus directly impacting their transmission and epidemic potential. Here, we compile and discuss the evidence supporting dengue-mediated changes in the yellow fever mosquito Aedes aegypti (L.), its primary vector, and evaluate whether the observed effects represent an evolved trait manipulation with epidemiological implications. Dengue infection appears to manipulate essential traits that facilitate vector–host contact, such as locomotor activity, host-seeking, and feeding behavior, but the underlying mechanisms are still not understood. Conversely, life-history traits relevant to vector population dynamics, such as survival, oviposition, and fecundity, appear to be negatively impacted by dengue virus. Overall, any detrimental effects on life-history traits may be a negligible cost derived from the virulence that dengue has evolved to facilitate its transmission by manipulating Ae. aegypti behavior and feeding performance. However, methodological disparities among studies render comparisons difficult and limit the ability to reach well-supported conclusions. This highlights the need for more standardized methods for the research into changes in virus-mediated traits. Eventually, we argue that the effects on life-history traits and behavior outlined here must be considered when assessing the epidemiological impact of dengue or other arbovirus–vector–host interactions.
The role of LRG1 and LRG2’s monopole in inferring the DESI 2024 BAO cosmology
Authors: Wang Zhengyi , Lin Shijie , Ding Zhejie , Hu Bin
Published: October 2024

The Dark Energy Spectroscopic Instrument (DESI) collaboration recently released its first year of data (DR1) on baryon acoustic oscillations (BAO) in galaxy, quasar, and Lyman-$\alpha$ forest tracers. When combined with cosmic microwave background (CMB) and Type Ia supernovae (SNIa) data, DESI BAO results suggest potential thawing behaviour in dark energy. Cosmological analyses utilize comoving distances along ($D_\mathrm{ H}$) and perpendicular to ($D_\mathrm{ M}$) the line of sight. Notably, there are $1\sim 2\sigma$ deviations in $D_\mathrm{ M}$ and $D_\mathrm{ H}$ from Planck cosmology values in the luminous red galaxies (LRG) bins LRG1 and LRG2.This study examines the role of LRG1 and LRG2 in diverging DESI 2024 BAO cosmology from Planck cosmology. We use angle-averaged distance $D_\mathrm{ V}$ and the ratio $F_{\rm AP}=D_\mathrm{ M}/D_\mathrm{ H}$, which are more directly related to the measured monopole and quadrupole components of the galaxy power spectrum or correlation function, instead of the officially adopted $D_\mathrm{ M}$ and $D_\mathrm{ H}$. This transformation aims to isolate the influence of monopoles in LRG1 and LRG2 on deviations from $w=-1$. Our findings indicate that removing the $D_\mathrm{ V}$ data point in LRG2 aligns DESI + CMB + SNIa data compilation with $w=-1$ within a $2\sigma$ contour and reduces the $H_0$ discrepancy from the Planck 2018 results from $0.63\sigma$ to $0.31\sigma$. Similarly, excluding the $D_\mathrm{ V}$ data point from LRG1 shifts the $w_0/w_a$ contour toward $w=-1$, although no intersection occurs. This highlights the preference of both LRG1 and LRG2 BAO monopole components for the thawing dark energy model, with LRG2 showing a stronger preference. We provide the $D_\mathrm{ V}$ and $F_{\rm AP}$ data and their covariance alongside this paper.
Hydrodynamic shielding in radiative multicloud outflows within multiphase galactic winds
Authors: Villares A S , Banda-Barragán W E , Rojas C
Published: October 2024

Stellar-driven galactic winds regulate the mass and energy content of star-forming galaxies. Emission- and absorption-line spectroscopy show that these outflows are multiphase and comprised of dense gas clouds embedded in much hotter winds. Explaining the presence of cold gas in such environments is a challenging endeavour that requires numerical modelling. In this paper, we report a set of 3D hydrodynamical simulations of supersonic winds interacting with radiative and adiabatic multicloud systems, in which clouds are placed along a stream and separated by different distances. As a complement to previous adiabatic, subsonic studies, we demonstrate that hydrodynamic shielding is also triggered in supersonic winds and operates differently in adiabatic and radiative regimes. We find that the condensation of warm, mixed gas in between clouds facilitates hydrodynamic shielding by replenishing dense gas along the stream, provided that its cooling length is shorter than the cloud radius. Small separation distances between clouds also favour hydrodynamic shielding by reducing drag forces and the extent of the mixing region around the clouds. In contrast, large separation distances promote mixing and dense-gas destruction via dynamical instabilities. The transition between shielding and no-shielding scenarios across different cloud separation distances is smooth in radiative supersonic models, as opposed to their adiabatic counterparts for which clouds need to be in close proximity. Overall, hydrodynamic shielding and re-condensation are effective mechanisms for preserving cold gas in multiphase flows for several cloud-crushing times, and thus can help understand cold gas survival in galactic winds.
Multiple collisions in N59 bubble: sequential cloud–cloud collisions
Authors: Chen En , Chen Xi , Chen Xuepeng , Fang Min , He Qianru
Published: October 2024

We report that the gas components in the N59 bubble suffered from sequential multiple cloud–cloud collision (CCC) processes. The molecular gas in the N59 bubble can be decomposed into four velocity components, namely Cloud A [95, 108] km s$^{-1}$, Cloud B [86, 95] km s$^{-1}$, Cloud C [79, 86] km s$^{-1}$, and Cloud D [65, 79] km s$^{-1}$. Four CCC processes occurred among these four velocity components, i.e. Cloud A versus Cloud B, Cloud A versus Cloud C, Cloud C versus Cloud D, and Cloud A versus Cloud D. Using the near- and mid-infrared photometric point source catalogues, we identified 514 young stellar object (YSO) candidates clustered in 13 YSO groups, and most of them ($\sim 60~{{\ \rm per\ cent}}$) were located at the colliding interfaces, indicating that they were mainly triggered by these four CCC processes. We also found that these four collisions occurred in a time sequential order: the earliest and most violent collision occurred between Cloud A and Cloud D about 2 Myr ago, then Cloud B collided with Cloud A about 1 Myr ago, and finally, Cloud C collided with Clouds A and D simultaneously about 0.4 Myr ago.
Constraining the properties of the thermonuclear burst oscillation source XTE J1814−338 through pulse profile modelling
Authors: Kini Yves , Salmi Tuomo , Vinciguerra Serena , Watts Anna L , Bilous Anna , Galloway Duncan K , van der Wateren Emma , Khalsa Guru Partap , Bogdanov Slavko , Buchner Johannes , Suleimanov Valery
Published: October 2024

Pulse profile modelling (PPM) is a comprehensive relativistic ray-tracing technique employed to determine the properties of neutron stars. In this study, we apply this technique to the Type I X-ray burster and accretion-powered millisecond pulsar XTE J1814−338, extracting its fundamental properties using PPM of its thermonuclear burst oscillations. Using data from its 2003 outburst, and a single uniform temperature hotspot model, we infer XTE J1814−338 to be located at a distance of $7.2^{+0.3}_{-0.4}$ kpc, with a mass of $1.21^{+0.05}_{-0.05}$ M$_\odot$ and an equatorial radius of $7.0^{+0.4}_{-0.4}$ km. Our results also offer insight into the time evolution of the hotspot but point to some potential shortcomings of the single uniform temperature hotspot model. We explore the implications of this result, including what we can learn about thermonuclear burst oscillation mechanisms and the importance of modelling the accretion contribution to the emission during the burst.
FlyRNAi.org 2025 update—expanded resources for new technologies and species
Authors: Hu Yanhui , Comjean Aram , Rodiger Jonathan , Chen Weihang , Kim Ah-Ram , Qadiri Mujeeb , Gao Chenxi , Zirin Jonathan , Mohr Stephanie E , Perrimon Norbert
Published: October 2024

The design, analysis and mining of large-scale ‘omics studies with the goal of advancing biological and biomedical understanding require use of a range of bioinformatics tools, including approaches tailored to needs specific to a given species and/or technology. The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) Functional Genomics Resources (https://fgr.hms.harvard.edu/tools) supports an increasingly broad group of technologies and species. Recently, for example, we expanded the database to include additional new data-centric resources that facilitate mining and analysis of single-cell transcriptomics. In addition, we have applied our approaches to CRISPR reagent and gene-centric bioinformatics approaches in Drosophila to arthropod vectors of infectious diseases. Building on our previous comprehensive reports on the FlyRNAi database, here we focus on new and updated resources with a primary focus on data-centric tools. Altogether, our suite of online resources supports various stages of functional genomics studies for Drosophila and other arthropods, and facilitate a wide range of reagent design, analysis, data mining and analysis approaches by biologists and biomedical experts studying Drosophila, other common genetic model species, arthropod vectors and/or human biology.
RMVar 2.0: an updated database of functional variants in RNA modifications
Authors: Huang Yuantai , Zhang Luowanyue , Mu Weiping , Zheng Mohan , Bao Xiaoqiong , Li Huiqin , Luo Xiaotong , Ren Jian , Zuo Zhixiang
Published: October 2024

Evaluating the impact of genetic variants on RNA modifications (RMs) is crucial for identifying disease-associated variants and understanding the pathogenic mechanisms underlying human diseases. Previously, we developed a database called RMVar to catalog variants linked to RNA modifications in humans and mice. Here, we present an updated version RMVar 2.0 (http://rmvar.renlab.cn). In this updated version, we applied an enhanced analytical pipeline to the latest RNA modification datasets and genetic variant information to identify RM-associated variants. A notable advancement in RMVar 2.0 is our incorporation of allele-specific RNA modification analysis to identify RM-associated variants, a novel approach not utilized in RMVar 1.0 or other comparable databases. Furthermore, the database offers comprehensive annotations for various molecular events, including RNA-binding protein (RBP) interactions, RNA–RNA interactions, splicing events, and circular RNAs (circRNAs), which facilitate investigations into how RM-associated variants influence post-transcriptional regulation. Additionally, we provide disease-related information sourced from ClinVar and GWAS to help researchers explore the connections between RNA modifications and various diseases. We believe that RMVar 2.0 will significantly enhance our understanding of the functional implications of genetic variants affecting RNA modifications within the context of human disease research.
The 2024 IPD-MHC database update: a comprehensive resource for major histocompatibility complex studies
Authors: Maccari Giuseppe , Robinson James , Barker Dominic J , Yates Andrew D , Hammond John A , Marsh Steven G E
Published: October 2024

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) serves as a comprehensive and expertly curated repository for major histocompatibility complex (MHC) sequences from non-human species, providing the necessary infrastructure and tools to study the function and evolution of this highly polymorphic genomic region. In its latest version, the IPD-MHC database has expanded both in content and in the tools for data visualization and comparison. The database now hosts over 18 000 MHC alleles from 125 species, organized into eleven taxonomic groups, all manually curated and named by the Comparative MHC Nomenclature Committee. A cetacean section has recently been included, offering researchers valuable data to study the immune system of whales, dolphins, and porpoises, as well establishing the official nomenclature platform for the Cetacea Leukocyte Antigens (CeLA). In response to user demand and reflecting broader trends in bioinformatics and immunogenetics, IPD-MHC now includes the predicted tertiary structure of over 8000 alleles and allows comparison and visualisation of allele variation within and between species at single residue resolution. These latest developments maintain the critically important link between official nomenclature of curated alleles and the ability to analyse this complex polymorphism using the most up to date methods within a single repository.
Luciano Berio
Authors: Peattie Thomas
Published: October 2024

Luciano Berio (b. 1925–d. 2003) was a leading figure in the postwar avant-garde. His subsequent reception and ongoing contributions to the history of 20th-century music during his own lifetime have only confirmed his reputation alongside Luigi Nono as one of the most important Italian composers of his generation. Berio studied composition in Milan with Giorgio Federico Ghedini and briefly at Tanglewood with Luigi Dallapiccola. The emergence of a distinct compositional voice by the early 1950s was shaped by an ambivalent if nevertheless foundational encounter with serial procedures, an engagement with folk materials, his experience in the electronic studio, lessons drawn from the fields of linguistics and semiotics, experiments with the human voice, and the idea of transcription. From the 1950s onward collaborative work assumed an important place in his creative practice, initially in the context of the Studio di Fonologia with Bruno Maderna and Umberto Eco. Collaborations with several prominent Italian writers soon followed, including Edoardo Sanguineti and Italo Calvino, both of whom provided texts for Berio’s most important stage works. A lifelong interest in collaborating with performers is best exemplified in his extraordinary creative partnership with Cathy Berberian (1925–1983). An extended stay in the United States (1960–1971), during which time he held teaching positions at Mills College and Juilliard, precipitated a return to Italy where he was once again able to devote the bulk of his energies to composition. During his final decades he received numerous awards and honors, including his appointment as the Norton Professor of Poetry at Harvard University (1993–1994). Berio’s compositional practice was guided by a set of specific concerns that included pursuing the wide transformational trajectory of a musical idea and imposing an inner logic and unity on heterogenous materials. A belief that counterpoint and analysis served as the basis of a composer’s craft is connected to his interest in the history of music, something that also informed his practice of reworking earlier pieces through the addition of layers of commentary that possess an “analytical” dimension (as in the Sequenzas recomposed as Chemins). Scholarship on Berio has long reflected a decidedly formalist orientation often rooted in sketch studies. While other perspectives have hardly been absent, more recent scholarship that situates his music in the larger social and political context of its time represents a welcome development. Although Berio’s music has given rise to a vast secondary literature in French, Italian, and German, the emphasis here is placed on English-language sources.
Learning Disabilities and Siblings
Authors: Ryan Tom
Published: October 2024

Sibling relationships are unique, and, when explored through a disability lens, they raise several important discussions that should be had. To unpack learning disability and siblings as a topic of research, it is necessary to ground the discussion both in sibling studies and in disability studies theory. This article starts with the key texts and journals, followed by theoretical discussions of both learning disability and siblinghood. Wider research into disability in families and siblings is then explored to provide further context. Following this, the article addresses learning disability and siblings specifically under the subsections of Childhood, Adulthood, Psychological and Outcome-Based Research, Care and support, and Everyday Life. It is important to acknowledge the overlap between literature on learning disabilities and autism; this reflects the estimated overlap between both labels (see Emerson et al. The Physical Health of British Adults with Intellectual Disability: Cross Sectional Study, 2016). Consequently, this bibliography will cite literature that references both learning disabilities and autism while focusing on the former. Alongside this, it should be acknowledged that this article employs the terminology “people with learning disabilities.” The term “intellectual disability” is often used outside of the United Kingdom; however, because the author is based in the United Kingdom, “learning disabilities” is the preferred terminology for this article.
Clinical impact of TP53 functional mutations in patients with metastatic colorectal cancer treated with bevacizumab and chemotherapy
Authors: Ruzzo Annamaria , Graziano Francesco , Palladino Silvia , Fischer Nicholas W , Catalano Vincenzo , Giordani Paolo , Malkin David , Tamburrano Tiziana , Patriti Alberto , Petrelli Filippo , Sarti Donatella , Chiari Rita
Published: October 2024

Background

Clinical and experimental studies indicate that the tumor protein p53 (TP53) gene loss of function due to missense mutations (MMs) may confer sensitivity to anti-angiogenics. This effect seems to be linked to cross-talk mechanisms among TP53, vascular endothelial growth factor (VEGF), and VEGF receptors. We investigated whether specific TP53 MMs are associated with clinical outcomes of patients with metastatic colorectal cancer (mCRC) treated with first-line chemotherapy plus Bevacizumab. The study focused on KRAS-mutated, liver-only mCRC cases as a homogeneous subgroup that may represent a relevant setting for exploring this association.

Materials and methods

MMs were identified on primary tumors. MMs were classified by mutant-specific residual transcriptional activity scores (TP53RTAS) as transcriptionally inactive (TP53inactive = TP53RTAS 0%) or active (TP53active = TP53RTAS ≥ 1%) and used for stratifying patients in progression-free survival (PFS), response rate, and overall survival (OS) analyses.

Results

The study population consisted of 62 patients. MMs were found in 39 cases (62%) with 16 having TP53inactive and 23 TP53active MMs. Patients with TP53inactive MMs showed better PFS in comparison with the remaining groups (wild-type and TP53active). This effect was retained in the multivariate model. A similar clinical impact was observed in the OS analysis. There was a significant difference in the overall response rate and rate of post-treatment resection of liver metastases between the TP53inactive and the wild-type or TP53active MMs cases.

Conclusions

Specific TP53 MMs may identify sub-groups of patients who benefit from Bevacizumab-based systemic therapy and these findings could lead to novel tailored treatment strategies in this setting.
Adorno on Non-identity
Authors: Cook Deborah
Published: October 2024

Working through several central texts by Adorno, this chapter will attempt to clarify the philosophical impetus behind his concept of non-identity, to reveal what animates it and what stands behind it. The first section of this chapter will show how the idea of non-identity addresses the perennial philosophical theme of unity and diversity. It will also discuss the role that contradiction, or antagonism, plays in bringing non-identity to the fore. Two subsequent sections in this chapter will offer a historical account of non-identity: they will examine where the idea first emerged in Adorno’s work and explore its more important philosophical and non-philosophical sources. Following this historical account of the idea of non-identity, the chapter will end by situating this idea within the broader context of Adorno’s critique of late capitalism because, as the author will argue, it is in this context alone that non-identity can be understood.
The Past, Present, and Future of Election Reform
Authors: Hasen Richard L.
Published: October 2024

This chapter considers what election “reform” is and why many Americans want it; who has successfully reformed election rules in the United States and how; the current Supreme Court’s role as a barrier to many progressive election reforms; and the future of election reform in a hyperdecentralized, polarized electoral system. Throughout American history, dissatisfaction with substantive policies and with political and economic inequality, including across race and gender, has fueled interest in changing political arrangements. Proposals for political change also prompt reactions by those opposing them. Some election reforms have already been enacted and implemented, while others have failed. Constitutional change is difficult given a cumbersome amendment process requiring supermajority support. Other reasons for failure include lack of sufficient popular support, self-interested legislative resistance to popular ideas and the absence of a direct democracy workaround, and language in the U.S. Constitution, at least as interpreted by the Supreme Court. In the current hyperpolarized political system, bipartisan cooperation on large-scale election reforms including constitutional amendments will be rare, and one-party supported statutory reforms or those passed through direct democracy will be more common. The biggest impediment to current progressive-oriented reform is the jurisprudence of the conservative Justices who make up a majority on the Supreme Court. It is harder to predict the success of election reforms in the longer term.
Redistricting Commissions
Authors: Manheim Lisa Marshall
Published: October 2024

Redistricting commissions represent a significant innovation in American election law. By shifting power away from state legislatures and toward entities specially designed to draw electoral lines, proponents hope to unlock the potential of institutional change. Born of reform across numerous jurisdictions, these commissions reflect a wide diversity of structures and features. Some of the most important differences involve how commissioners are selected, how much autonomy each commission exercises, and the rules governing each entity’s internal voting processes. Scholars have examined these legal differences and their implications for redistricting. They have also explored, more broadly, the normative underpinnings of these reforms as well as commissions’ empirical outputs. Notwithstanding this rich body of scholarship, trends dominating American politics, including those associated with rising polarization, have outpaced the literature in potentially important ways. At least three related phenomena—the threat of partisan capture, the variable durability of reform, and the inherent limitations of commissions—complicate the work of commissions and their potential going forward and, accordingly, warrant further examination.
Political Corruption
Authors: Gilbert Michael D. , Hellman Deborah
Published: October 2024

This chapter studies political corruption and its many relationships to the law of democracy. It begins with bribery laws, which forbid officials from selling official acts. Federal bribery law is circular, reflecting uncertainty and disagreement around the concept of bribery itself. Next, the chapter studies campaign finance regulations, which raise First Amendment concerns but are nevertheless often justified on anticorruption grounds. Then the chapter examines vote buying, which relates to the secret ballot and the complicated connections between corruption and publicity. The chapter addresses the constitutional dimensions of corruption, including its role in impeachment and the Emoluments Clauses, and it concludes with a discussion of the appearance of corruption, a concern that surfaces in many areas, including judicial recusal and misuse of office. The law of political corruption is often vague, and scholars disagree about the very nature of corruption. This leaves much authority in the hands of the actors, including judges, empowered to define corruption in practice.
The Theoretical Foundations of Campaign Finance Regulation
Authors: Dawood Yasmin
Published: October 2024

This chapter discusses the theoretical foundations of campaign finance regulation with a particular focus on the central concepts—political equality, liberty, corruption, participation, representation, free speech, accountability, political influence, and democracy—that have animated scholarly debates. The chapter begins by outlining the key Supreme Court decisions on the constitutionality of campaign finance measures and the central concepts that have emerged from these cases. It then turns to the classic debate between libertarian and egalitarian approaches to campaign finance regulation. It also traces the egalitarian and libertarian strands in the Supreme Court’s decisions. The chapter subsequently analyzes the concept of corruption. It sets out various categorizations of corruption and addresses why corruption is wrong. The chapter then turns to the relationship between campaign finance and democracy, exploring various issues including political inequality, legislative skew, plutocracy, participation, and representation. Finally, the chapter considers the First Amendment and its application to campaign speech and elections. It canvasses debates on various topics, including money as speech, disclosure, electoral exceptionalism, electoral integrity, and the right of participation. The conclusion outlines two avenues of ongoing research: the challenges of social media and judicial deregulation, respectively, which have broad implications for campaign finance.
Voting Under State Law
Authors: Greenwood Ruth
Published: October 2024

As the environment for litigation and legislative advocacy becomes increasingly hostile at the federal level, many have turned to state legislative advocacy and state court litigation to protect and promote voting rights. This chapter does not discuss every important reform, or every troubling restriction, being considered at the state level, but rather outlines some key categories of laws that help, or hinder, historically disenfranchised communities with respect to voting. The chapter focuses on some of the main ways that people of color, people with disabilities, young voters, and people involved in the criminal justice system are affected by state voting laws. It also looks at the relatively recent development of state voting rights acts that seek to provide protections for people of color as federal protections are eroded and even go well beyond the types of protections that have historically been provided by federal legislation.
Ontological Resilience
Authors: Weedman Arthur Kathryn , Ethiopia Tocha Yohannes
Published: October 2024

Histories generally portray southern Ethiopians as pagans who lacked kings because they rely on the historical accounts of their northern Abyssinian conquerors, who adopted Christianity in the first century AD. Justified by a call to spread Christianity and suffering the threat of famine and disease to his empire, Abyssinian emperor Menelik II (1889–1913) conquered and colonized southern Omotic-speaking polities, who cultivated a drought-resistant crop, enset (Ensete ventricosum). According to most Ethiopian histories, Boreda were one of the southern Omotic societies, who quickly succumbed to conquest, adopted new agricultural technologies, and paid tribute and corvée labor. Boreda identity and history are entwined with farming enset, a relationship that provided food security, structured their historic settlement landscape, and charted their relationship with technology, each other, and outsiders. The authors argue that everyday practices, such as the farming of enset, are spaces within which Indigenous peoples frame and materialize ontological resilience against colonialism, religious conversion, and persecution. Boreda oral traditions, life histories, and daily practices support their efforts to resist settlers and richly inform the archaeology of their historic places, Bayira Deriya.