bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raccoons Reveal Hidden Diversity in Trabecular Bone Development
Authors: Reinecke T , Angielczyk K D 
Published: October 2024

Synopsis
Trabecular bone, and its ability to rapidly modify its structure in response to strain exerted on skeletal elements, has garnered increased attention from researchers with the advancement of CT technology that allows for the analysis of its complex lattice-like framework. Much of this research has focused on adults of select taxa, but analysis into trabecular development across ontogeny remains limited. In this paper, we explore the shift in several trabecular characteristics in the articular head of the humerus and femur in Procyon lotor across the entirely of the species’ lifespan. Our results show that while body mass plays a role in determining trabecular structure, other elements such as bone growth, increased activity, and puberty result in trends not observed in the interspecific analysis of adults. Furthermore, differences in the trabeculae of the humerus and femur suggest combining distinct boney elements in meta-analysis may obfuscate the variety in the structures. Finally, rates at which fore and hindlimb trabeculae orient themselves early in life differ enough to warrant further exploration to identify the currently unknown causes for their variation.
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

Abstract
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 (&lt;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

Abstract

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

Abstract

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 &gt; 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

Abstract
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

Abstract
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 &gt; C. pilosula &gt; 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 &gt; 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.