bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expectation elicits music-evoked chills
Authors: de Fleurian Rémi , Clemente Ana , Benetos Emmanouil , Pearce Marcus T. 
Published: October 2024

AbstractMusic-evoked chills (MECs) are physiological responses to pleasurable events in music. Existing research on properties of music that elicit MECs has focused on low-level acoustic features in small samples of music. We created a large dataset of over 1,000 pieces of music timestamped with MECs and used computational methods to predict MEC onsets from both low-level acoustic features and high-level musical expectations. A machine learning classifier was trained to distinguish MEC onsets from non-MEC passages in the same pieces. The results show that MEC onsets are predicted better than chance and corroborate evidence for acoustic elicitors of chills with a much larger dataset. They also produce new empirical evidence that MECs are elicited by expectation, which is a more effective predictor of MEC onsets than acoustic elicitors, and may generalise to pleasurable experience in other domains such as language comprehension or visual perception.
Cysimiditides: RiPPs with a Zn-tetracysteine motif and aspartimidylation
Authors: Zhu Angela , Cao Li , Do Truc , Link A. James 
Published: October 2024

AbstractAspartimidylation is a post-translational modification found in multiple families of ribosomally synthesized and post-translationally modified peptides (RiPPs). We recently reported on the imiditides, a new RiPP family in which aspartimidylation is the class-defining modification. Imiditide biosynthetic gene clusters encode a precursor protein and a methyltransferase that methylates a specific Asp residue, converting it to aspartimide. A subset of imiditides harbor a tetracysteine motif, so we have named these molecules cysimiditides. Here, using genome mining we show that there are 56 putative cysimiditides predicted in publicly available genome sequences, all within actinomycetota. We successfully heterologously expressed two examples of cysimiditides and showed that the major products are aspartimidylated and that the tetracysteine motif is necessary for expression. Cysimiditides bind a Zn2+ion, presumably at the tetracysteine motif. Usingin vitroreconstitution of the aspartimidylation reaction, we show that Zn2+is required for methylation and subsequent aspartimidylation of the precursor protein. An AlphaFold 3 model of the cysimiditide fromThermobifida cellulosilyticashows a hairpin structure anchored by the Zn2+-tetracysteine motif with the aspartimide site in the hairpin loop. An AlphaFold 3 model of this cysimiditide in complex with its cognate methyltransferase suggests that the methyltransferase recognizes the Zn2+-tetracysteine motif to correctly dock the precursor protein. Cysimiditides expand the set of experimentally-confirmed RiPPs harboring aspartimides, and represent the first RiPP class that has an obligate metal ion.Table of Contents Figure
Automated Tumor and FUS Lesion Quantification on Multi-frequency Harmonic Motion and B-mode Imaging Using a Multi-modality Neural Network
Authors: Hu Shiqi , Liu Yangpei , Li Xiaoyue , Konofagou Elisa E. 
Published: October 2024

AbstractHarmonic Motion Imaging (HMI) is an ultrasound elasticity imaging method that measures the mechanical properties of tissue using amplitude-modulated acoustic radiation force (AM-ARF). By estimating tissue’s on-axis oscillatory motion, HMI-derived displacement images represent localized relative stiffness and can predict the tumor response to neoadjuvant chemotherapy (NACT) and monitor focused ultrasound (FUS) ablation therapy. Multi-frequency HMI (MF-HMI) excites tissue at various AM frequencies simultaneously, which allows for image optimization without prior knowledge of inclusion size and stiffness. However, challenges remain in size estimation as inconsistent boundary effects result in different perceived sizes across AM frequencies. Herein, we developed an automated tumor and FUS lesion quantification method using a transformer-based multi-modality neural network, HMINet. It was trained on 380 pairs of MF-HMI and B-mode images of phantoms andin vivoorthotopic breast cancer mice (4T1). Test datasets included phantoms (n = 32),in vivo4T1 mice (n = 24), breast cancer patients (n = 16), and a FUS-induced lesion, with average segmentation accuracy (Dice Similarity Score) of 0.95, 0.86, 0.82, and 0.87, respectively. To increase the generalizability of HMINet, we applied a transfer learning strategy, i.e., fine-tuning the model using patient data. For NACT patients, the displacement ratios (DR) between the tumor and surrounding tissue were calculated based on HMINet-segmented boundaries to predict tumor response based on stiffness changes.
Overexpression of Ribosomal Proteins Leads to Zn Resistance inEscherichia coli
Authors: Kosaki Tomoki , Shirakawa Riko , Ishikawa Kazuya , Furuta Kazuyuki , Kaito Chikara 
Published: October 2024

AbstractKnockout of ribosomal protein bL36 (RpmJ) leads to Zn resistance inEscherichia coli, and the expression of ribosomal protein genes other than RpmJ increase in therpmJ-knockout strain. In this study, we examined whether the overexpression of ribosomal proteins causes Zn resistance using anE. colioverexpression gene library (ASKA clone library). The overexpression of 48 of the 54 ribosomal proteins led to Zn resistance. However, the overexpression of proteins other than ribosomal proteins did not lead to Zn resistance, suggesting that Zn resistance is a phenomenon specific to the overexpression of ribosomal proteins. In addition, the overexpression of ribosomal proteins did not lead to resistance to metal ions other than Zn (Cu2+, Ni2+, Mn2+, and Ag+), suggesting a Zn-specific resistance mechanism. Deletion of ZntA, a Zn efflux pump, resulted in the loss of Zn resistance in a ribosomal protein-overexpressing strain. Deletion of Lon protease, which is responsible for degrading misfolded proteins, in a ribosomal protein-overexpressing strain resulted in the accumulation of overexpressed ribosomal proteins and loss of Zn resistance. These results suggest that the overexpression of ribosomal proteins leads to Zn resistance inE. coli viaZntA and Lon protease.ImportanceThe ribosome is a complex comprising ribosomal RNAs and more than 50 types of ribosomal proteins. Ribosomal proteins play an important role in ribosomal function responsible for protein translation; however, their involvement in other cellular processes is not fully understood. Based on the finding that ribosomal protein expression increases in a Zn-resistantE. colimutant, we analyzed 54 ribosomal proteins and found that the overexpression of 48 ribosomal proteins led to Zn resistance. This finding suggests a role for ribosomal proteins in resistance to zinc stress.
Protein–protein interactions shapetrans-regulatory impact of genetic variation on protein expression and complex traits
Authors: Li Jinghui , Li Yang I. , Liu Xuanyao 
Published: October 2024

AbstractMost genetic variants influence complex traits by affecting gene regulation. Yet, despite comprehensive catalogs of molecular QTLs, linking trait-associated variants to biological functions remains difficult. In this study, we re-analyzed large maps of protein QTLs (pQTLs) to show that genes withtrans-pQTLs but withoutcis-pQTLs are under strong selective constraints and are highly enriched in GWAS loci. We found thattrans-pQTLs and theirtranstargets are highly enriched in interacting protein pairs, andtrans-pQTLs in coding regions are significantly enriched at protein-protein interactions (PPI) interfaces. By leveraging existing PPI annotations fortrans-pQTL mapping, we identified 26,028trans-pQTLs influencing 1,061 PPI clusters. Thetrans-pQTLs of PPIs colocalized with 66% GWAS loci per trait on average for 50 complex traits, helping in many cases to link GWAS loci to cellular function. Finally, we identifiedtrans-pQTL effects at multiple autoimmune GWAS loci that converge on the same PPIs, pinpointing protein complexes and signaling pathways that show promising therapeutic target potential.
Growth compensation upon changes in tissue size in theDrosophilaabdomen
Authors: Ferreira Ana , Cairoli Andrea , Mangione Federica , Holder Maxine V. , Ainslie Anna , Aerne Birgit L. , Salbreux Guillaume , Tapon Nicolas 
Published: October 2024

SUMMARYAttaining the appropriate size during development is essential for the function of animal tissues and organs. Robust tissue size control implies the existence of compensatory mechanisms that allow developing systems to recover from growth perturbations. However, the difficulty of directly observing normal or compensatory developmental growth means we have little understanding of the cellular behaviours that confer robustness to tissue size control. Here, we study how growth perturbations affect proliferation kinetics and the timing of growth termination ofDrosophilahistoblasts, the progenitors that give rise to the adult abdominal epidermis. Histoblasts undergo extensive growth and proliferation during the pupal stage, which is accessible for long-term live-imaging and precise quantitative analysis. By manipulating cell number or volume prior to the pupal growth phase, we changed the starting size of the abdomen primordium, then observed how the histoblasts adapted to these changes by altering their growth dynamics. We show that, upon a decrease in starting tissue size, the histoblasts compensate by extending their temporal proliferative window, undergoing additional cell cycles, as well as increasing their apical area to maximise coverage of the abdominal surface. When initial tissue size is increased, the histoblasts undergo fewer division cycles and arrest proliferation earlier than normal. Thus, the proliferative window of this tissue is flexible enough to buffer for changes in tissue size. Our data also suggest that the histoblasts sense both spatial and temporal cues to arrest their growth at the appropriate time and ensure accurate tissue size control.
Expression of endogenousAnopheles gambiaemicroRNAs using anAnopheles gambiaedensovirus (AgDNV) intronic expression system
Authors: Johnson Rebecca M. , Metz Hillery C. , Suzuki Yasutsugu , McLean Kyle J. , Rasgon Jason L. 
Published: October 2024

AbstractAnopheles gambiaedensovirus (AgDNV) is a highly species-specific parvovirus that reaches high titers in adultAnopheles gambiaemosquitoes with few transcriptomic effects and no significant fitness effects. Given these characteristics, AgDNV has been proposed as a viral vector for basic research and mosquito control. Previous work created an AgDNV co-expression system with a wild-type AgDNV helper plasmid and a transducing enhanced green fluorescent protein (EGFP) expressing plasmid that can be used to co-transfect cells to generate infectious recombinant transducing AgDNV virions. Generated virions infect theAn. gambiaemidgut, fat body, and ovaries, yet this viral vector system is limited in the size of transgenes that can be expressed due to capsid packaging limitations. Considering these size constraints, we created an artificial intron within the EGFP gene of the transducing construct that can express small pieces of genetic material such as microRNAs (miRNAs), microRNA sponges, or other small sequences. Placement of this intron in EGFP created a fluorescent reporter such that incorrect splicing produces a frameshift mutation in EGFP and an early stop codon whereas correct splicing results in normal EGFP expression and co-transcription of the intronic genetic cargo. A selection of miRNAs with predicted or demonstrated importance in mosquito immunity and reproduction with expression localized to the fat body or ovaries were chosen as intronic cargo, construct expression and splicing evaluated, and the impact of miRNA expression on putative miRNA targets was measuredin vitroandin vivo. While the intron was correctly spliced in cells and mosquitoes, miRNA delivery resulted in inconsistent changes to miRNA and target gene transcript levels—possibly due to organ-specific miRNA expression or miRNA-target gene sequence mismatch. However, with optimization this viral vector and developed intron have potential as an expression tool withinAn. gambiaemosquitoes or cells.
PPARγ downregulation in colonic CD8+ T cells results in epithelial barrier disruption in people with HIV on antiretroviral therapy
Authors: Das Adhikari Upasana , Froehle Leah M. , Pipkin Alexandra N. , Baharlou Heeva , Linder Alice H. , Shah Palak , Hussey Amanda , Zhang Qiming , Nyquist Sarah , Khwaled Saleh , Chi Fangtao , Goswami Swagata , Dieffenbach Thomas J. , Read Benjamin J. , Kim Byungji , Irvine Darrell , Asowata Osaretin , Ladinsky Mark , Bjorkman Pamela , Madela Fusi , Khader Shakeel , Shalek Alex , Ghebremichael Musie , Kloverpris Hendrik , Ringel Alison E , Yilmaz Ömer H. , Kwon Douglas S. 
Published: October 2024

SUMMARYA hallmark of HIV infection is disruption of intestinal barrier integrity that persists in people with HIV (PWH) despite treatment with antiretroviral therapy (ART). This disruption is central to HIV disease progression, yet the causes remain incompletely understood. We report a novel mechanism by which immunometabolic defects in colon resident CD8+ T cells in PWH lead to intestinal epithelial apoptosis and disruption of intestinal barrier integrity. We show that in PWH, these cells downregulate the lipid sensor peroxisome proliferator-activated receptor-γ (PPARγ), which results in reduced intracellular lipid droplets, impaired fatty acid oxidation, and acquisition of lipids by CD8+ T cells from intestinal epithelial cells, which then contributes to epithelial cell death. Our findings indicate that HIV-associated immunometabolic dysregulation of colon CD8+ T cell leads to loss of intestinal epithelial homeostasis. These results identify potential new strategies to reduce comorbidities in PWH and other disorders with disrupted intestinal barrier integrity.
Building a community-driven bioinformatics platform to facilitateCannabis sativamulti-omics research
Authors: Mansueto Locedie , Kretzschmar Tobias , Mauleon Ramil , King Graham J. 
Published: October 2024

AbstractGlobal changes in Cannabis legislation after decades of stringent regulation, and heightened demand for its industrial and medicinal applications have spurred recent genetic and genomics research. An international research community emerged and identified the need for a web portal to host Cannabis-specific datasets that seamlessly integrates multiple data sources and serves omics-type analyses, fostering information sharing.The Tripal platform was used to host public genome assemblies, gene annotations, QTL and genetic maps, gene and protein expression, metabolic profile and their sample attributes. SNPs were called using public resequencing datasets on three genomes. Additional applications, such as SNP-Seek and MapManJS, were embedded into Tripal. A multi-omics data integration web-service API, developed on top of existing Tripal modules, returns generic tables of sample, property, and values. Use-cases demonstrate the API’s utility for various -omics analyses, enabling researchers to perform multi- omics analyses efficiently.
The artisanal underground: gold, subsistence, and subsurface materiality in Colombia
Authors: Jonkman Jesse 
Published: October 2024

AbstractThis article focuses on subsurface materiality to explore how small‐scale gold miners in Colombia navigate formal politics. In much critical research, the underground appears as a space of great developmentalist ambition, whose resources enable corporate expansion and bureaucratic rule. Here I take a slightly different route, as I demonstrate that subterranean matter makes possible ways of knowing and working that are anathema to a pro‐corporate legal regime. More specifically, I maintain that Colombian small‐scale miners experience the underground as invisible and unruly matter, and I show that this experience mediates their everyday criticism of, and resistance to, state governance.
An experimental test on the hypothesis of strategic uncertainty
Authors: Li Bin , Wang Meng , Xu Tingyu 
Published: October 2024

AbstractThis study tests the influential hypothesis of strategic uncertainty (HSU) on the topic of bubble formation. We argue that if HSU holds, it shall apply to a stricter situation in which subjects in the market are rational, but none of them know the rationality distribution of others. The research strategies of exclusion and analogy are adopted to create a market that satisfies the two prerequisites of HSU. Briefly, a cohort of 24 participants in the same group is separated equally into three small groups using a pre‐determined rule within a 20‐period treatment. Group #1 is our primary concern, and its members comprise participants whose units of assets are zero with an auxiliary criterion by subjects' performance at the end of Period 5. Across sessions, we determine whether the regrouping criteria and group tags are displayed to subjects to control how hard it is for a trader to judge the distribution of others in his/her group. We observe that mispricing generally vanishes in both the experimental and control groups. This result delivers a negative judgement of HSU at the aggregate level. Observations at the individual level and the robustness experiments deliver the same judgement.
Morphological and functional characterization of circulating hemocytes in Tribolium castaneum larvae
Authors: Wang Suisui , Miao Shiyuan , Li Yusi , Wang Jianhui , Li Chengjun , Lu Yujie , Li Bin 
Published: October 2024

AbstractHemocytes are pivotal in the immune response of insects against invasive pathogens. However, our knowledge of hemocyte types and their specific function in Tribolium castaneum, an increasingly important Coleoptera model insect in various research fields, remains limited. Presently, a combination of morphological criteria and dye‐staining properties were used to characterize hemocyte types from T. castaneum larvae, and 4 distinct types were identified: granulocytes, oenocytoids, plasmatocytes and prohemocytes. Following different immune challenges, the total hemocyte counts declined rapidly in the initial phase (at 2 h), then increased over time (at 4 and 6 h) and eventually returned to the naive state by 24 h post‐injection. Notably, the morphology of granulocytes underwent dramatic changes, characterized by an expansion of the surface area and an increased production of pseudopods, and with the number of granulocytes rising significantly through mitotic division. Granulocytes and plasmatocytes, the main hemocyte types in T. castaneum larvae, can phagocytose bacteria or latex beads injected into the larval hemolymph in vivo. Furthermore, these hemocytes participate in the encapsulation and melanization processes in vitro, forming capsules to encapsulate and melanize nickel–nitrilotriacetic acid (Ni–NTA) beads. This study provides the first comprehensive characterization of circulating hemocytes in T. castaneum larvae, offering valuable insights into cell‐mediated immunity in response to bacterial infection and the injection of latex beads. These results deepen our understanding of the cellular response mechanisms in T. castaneum larvae and lay a solid foundation for subsequent investigations of the involvement of T. castaneum hemocytes in combating pathogens.
Biomass consumption, foraging activity and harvesting patterns in two sympatric leaf‐cutting ant species in a Salicaceae plantation in Argentina
Authors: Jiménez Nadia L. , Sánchez‐Restrepo Andrés F. , Guala Mariel E. , Battagliotti Cristian , Farji‐Brener Alejandro G. , Calcaterra Luis A. 
Published: October 2024

Abstract
Leaf‐cutting ants (LCA) are one of the most important pests in the Neotropics region. To estimate the potential biomass consumption by LCA on Salicaceae plantations in the lower delta of the Paraná River, we studied the foraging activity and harvesting patterns of Acromyrmex lundii (Guérin‐Méneville, 1838) and Acromyrmex ambiguus (Emery, 1888) (Hymenoptera: Formicidae) in a 14‐year‐old poplar plantation in Argentina.
Foraging activity (workers/time), harvested vegetal biomass (dry weight/time) and climatic conditions (temperature and relative humidity) were monitored daily and seasonally in nests from autumn 2016 to summer 2017.
The two sympatric species harvested a similar quantity of dry biomass throughout the year (4.9–6.0 kg/colony). Although both species were active in all seasons, their foraging activity was higher in spring and summer, but they avoided extreme temperatures. The accumulated biomass harvested for both species was higher in summer (28.8 and 25.7 g/colony/day, for Ac. ambiguus and Ac. lundii, respectively). However, Ac. lundii harvested three times more biomass than Ac. ambiguus in spring (30.3 and 13.1 g/colony/day, respectively).
Although the highest consumption on the vegetation occurred in summer, control tasks should be started during spring (sprouting phase), the most vulnerable period for Salicaceaes. The consumption of new leaves in spring is critical for tree growth, survival and wood production, especially by Ac. lundii, the most detrimental species during this season.
Trophic Structure and Dietary Overlap in the Sympatric Skinks Trachylepis punctatissima and Trachylepis varia From Central South Africa
Authors: Heideman Neil , Bates Michael , Zhao Zhongning 
Published: October 2024

ABSTRACTDiet diversity and overlap was investigated in the sympatric skinks Trachylepis punctatissima and Trachylepis varia from central South Africa using stomach and intestinal contents of museum specimens. Simpson's Index and the Shannon–Wiener Index were used to determine their food niche breadths and Pianka's Index to determine the extent to which they shared the food resource. Food items were identified from head capsules, mouthparts and appendages to order level. The two species contained similar prey types with T. varia having the wider niche breadth. Females also had wider niche breadths than males and isopterans were present in significantly higher quantities than the rest of the food items in both species. Larvae were found in both, but arachnids only in T. varia. Trophic niche overlap between the two was fairly high (Pianka's Index, 0.6915) and therefore did not support the hypothesis that similar species sharing a food resource should have well differentiated diets to reduce competition. This finding however requires further verification as the two species may consume different species of the corresponding orders identified. Intraspecifically trophic niche overlap between the sexes was low (T. punctatissima, 0.3889; T. varia, 0.4633) suggesting strong competition for the food resource. Notably lower niche breadth in males compared to females may be due to morphological and behavioural differences and should be further investigated.