bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeny in cages: Age-structure and timing of attractant availability impacts fertile egg production in the black soldier fly,Hermetia illucens
Authors: Lemke N. B. , Li C. , Dickerson A. J. , Salizar D. A. , Rollinson L. N. , Mendoza J. E. , Miranda C. D. , Crawford S. , Tomberlin J. K. 
Published: August 2024

AbstractAdult behavior is a growing area of interest for those researching the black soldier fly,Hermetia illucens(L.) (Diptera: Stratiomyidae), which is affected by underlying demography and spatiotemporal patterns. This greenhouse experiment examined the interaction of age-related effects that can accrue within heterogeneous breeding populations and the potential benefits of delaying an oviposition attractant in concert with restricting mean cohort age. The impetus for this investigation was because if flies are introduced into a mating-cage before old flies are removed or culled, this creates a population of mixed-age and mating-status. We hypothesized this potentially reduces quality among available mate choices, especially in small cages where flies might not be able to spatially segregate. Metrics for fitness included copulation frequency, oviposition frequency, weight of eggs produced, and hatch percentage. “Same”-aged cohorts (maximum 4-d-old at introduction) performed better than highly heterogeneous (1-16-d-old) “mixed” cohorts by mating 2.32-times more frequently and laying 6.58-times more eggs that were 1.17-times more fertile, despite 1.41 fewer observed oviposition events. Delaying the attractant had a significant effect on egg collection weight and led to 1.25-times higher egg yields for same- age populations compared to mixed-aged cohorts where the delaying the attractant had no significant effect. These results are likely due in part to an immediate desire to lay eggs by older females as well as haphazard egg laying in cage material, which was 2.09-times higher for mixed cohorts. The results highlight the importance of constraining the age of breeding populations and removing old adults from cages to improve yields and better manipulate behavior. For those for whom this is logistically unfeasible, providing an attractant box initially and continuously may be the preferred method to trap more eggs from heterogeneous populations.
Rapid Parallel Visual Presentation Provides a New Perspective on Relative Clause Processing in Mandarin Chinese
Authors: Dunagan Donald , McLendon Jill , Jordan Tyson , Chacón Dustin A. 
Published: August 2024

AbstractA fundamental question in language processing research is the degree to which the acceptability and ease of interpretation of a sentence are affected by the moment-by-moment memory encoding and retrieval processes needed to process it in time, vs. the properties of the linguistic representation itself, such as syntactic complexity. This manuscript investigates relative clauses, a crucial testing ground for theories of language processing, using parallel presentation, a technique in which the key elements of the target syntactic dependency are displayed to the visual system at the same time. Compared to serial presentation, parallel presentation mitigates the extent to which complex memory operations must be deployed to process the structure word-by-word. We report on an electroencephalography (EEG) experiment in Mandarin Chinese. Participants were presented with sentences which contained either a subject- or object-modifying subject- or object-extracted relative clause. Sentence presentation was split across two separate screens, with each screen being displayed only for 166ms on average. We find a behavioral preference for subject-extracted relative clauses and distinct EEG signatures for subject- and object-extracted relative clauses. Together, these results – on account of the parallel presentation scheme applied here – provide support for the independent contribution of linguistic representation in processing difficulty and the perspective that relative clause processing involves more than the factors that word by word accounts of this phenomenon would suggest. Further, the EEG result contributes to a growing body of electrophysiology literature attempting to illuminate the processing mechanisms deployed in the context of parallel presentation.
Divergent realized ecological niches of sister species of the Antarctic amphipod genusCharcotia
Authors: Aerts Dorien , Kolder Aaron , Lepoint Gilles , Michel Loïc N. , Schön Isa 
Published: August 2024

AbstractClimate change and resource exploitation in the Southern Ocean are important Anthro-pogenic pressure on Antarctic food webs. Understanding the eco-functional roles of Antarctic communities is essential for ecosystem management and conservation. Amphipods are among the most dominant and ecologically important benthic taxa in the Southern Ocean. The amphipod genusCharcotiais part of the scavenger guild playing a dominant role in nutrient recycling. To study the trophic habits of two sister species,C. amundseniandC. obesa, stable isotope ratios of carbon and nitrogen were investigated along geographical and bathymetrical gradients.Charcotia obesabelongs to the fourth andC. amundsenito the fifth trophic level, based on significant differences in δ15N. Benthic primary producers dominate the diet in both species as derived from their δ13C values.Charcotia obesa, the species with the narrowest depth range, did not show a depth-related pattern in isotopic ratios. An increasing geographic gradient of both δ15N and δ13C values was observed forC. obesa, ranging from the northern most tip of the Western Antarctic Peninsula to the southwestern most part of the Bellings-hausen Sea. This might be linked to nutrient rich glacial meltwater in the latter part of the Southern Ocean. Nitrogen stable isotope ratios ofC. amundsenishowed a significant difference between Crown Bay and the other locations; this might be explained by the close location of the Filchner Area to nutrient rich upwelling in the Weddell Sea Gyre. Our study provides evidence for niche differentiation between two closely related amphipod species. Incorporation of additional samples from other locations and depth ranges in combination with isotope analysis and DNA-based prey identification might clarify the trophic position of benthic amphipods.
Population dynamics in spatial suppression gene drive models and the effect of resistance, density dependence, and life history
Authors: Zhang Xinyue , Sun Weitang , Kim Isabel K. , Messer Philipp W. , Champer Jackson 
Published: August 2024

AbstractDue to their super-Mendelian inheritance, gene drive systems have the potential to provide revolutionary solutions to critical public health and environmental problems. For suppression drives, however, spatial structure can cause “chasing” population dynamics that may postpone target population elimination or even cause the drive to fail. In chasing, wild-type individuals elude the drive and recolonize previously suppressed areas. The drive can re-enter these recolonized areas, but often is not able to catch up to wild-type and finally eliminate it. Previous methods for chasing detection are only suitable to limited parameter ranges. In this study with expanded parameter ranges, we found that the shift from chasing dynamics to static equilibrium outcomes is continuous as drive performance is reduced. To quantify this, we defined a Weighted Average Nearest Neighbor statistic to assess the clustering degree during chasing, while also characterizing chasing by the per-generation chance of population elimination and drive loss. To detect chasing dynamics in local areas and to detect the start of chasing, we implemented Density-Based Spatial Clustering of Applications with Noise. Using these techniques, we determined the effect of arena size, resistance allele formation rate in both the germline and in the early embryo from maternally deposited Cas9, life history and reproduction strategies, and density-dependent growth curve shape on chasing outcomes. We found that larger real-world areas will be much more vulnerable to chasing and that species with overlapping generations, fecundity-based density dependence, and concave density-dependent growth curves have smaller and more clustered local chasing with a greater chance of eventual population elimination. We also found that embryo resistance and germline resistance hinder drive performance in different ways. These considerations will be important for determining the necessary drive performance parameters needed for success in different species, and whether future drives could potentially be considered as release candidates.
Differential induction ofMedicago truncatuladefence metabolites in response to rhizobial symbiosis and pea aphid infestation
Authors: Benjamin Goodluck , Pacoud Marie , Boutet Stéphanie , Clement Gilles , Brouquisse Renaud , Gatti Jean-Luc , Poirié Marylène , Frendo Pierre 
Published: August 2024

SummaryLegumes symbiosis with rhizobial nitrogen-fixing bacteria enable them to grow in nitrate-depleted soils. Rhizobial symbioses also induces systemic plant defence against bioagressors.We investigate how nitrogen-fixing symbiosis (NFS) in the legumeMedicago truncatulacan prime plant defence against the pea aphidAcyrthosiphon pisum. We analysed metabolite modification both by LC-MS and GC-MS and defence pathway gene expression by qPCR in leaves of both NFS and nitrate-fed (non-inoculated; NI) plants after aphid infestation (Amp).The accumulation of primary and secondary metabolites was modulated by both NFS and aphid infestation. 62 defense-related metabolites such as salicylate, pipecolate, gentisic acid and several soluble sugars were differentially regulated by aphid infestation in both NFS and NI conditions. 19 metabolites, including triterpenoid saponins, accumulated specifically in NFS_Amp conditions. Gene expression analysis showed that aphid-infested plants exhibited significantly higher expression ofChalcone isomerase,flavonol synthase,hydroxyisoflavone-O-methyl transferaseandPterocarpan synthase, whileD-pinitol dehydrogenasewas only significantly induced in NI infested leaves.Our data suggest that NFS, in addition to being a plant nitrogen provider, stimulates specific legume defenses upon pest attack and should also be considered as a potential tool in Integrated Pest Management strategy.
Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP
Authors: Tidwell Alyssa K. , Faust Evelyn , Eckert Carrie A. , Guss Adam M. , Alexander William G. 
Published: August 2024

AbstractBacterial DNA methylation is involved in diverse cellular functions ranging from modulation of gene expression, DNA repair, and restriction-modification systems for defense against viruses and other foreign DNA. Methylome analysis determines sites within a bacterial chromosome that are methylated, revealing motifs that may be targeted by native restriction enzymes. Identification of these motifs is therefore critical to making an organism genetically tractable, where mimicking the methylome patterns inEscherichia coliallows plasmid DNA to be protected from restriction in the target organism and can therefore drastically enhance transformation efficiency. Oxford Nanopore Technologies (ONT) sequencing can detect methylated bases during sequencing, but software is needed to identify the corresponding methylated motifs within the data. Here, we develop MIJAMP (MIJAMP Is JustA MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT’s Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating false, under-, or overexplained motifs. MIJAMP can also report methylation data on a specific, user-defined motif. Using MIJAMP, we determined the methylated motifs both in a control strain (wild typeE. coli) and inPicosynecococcussp. strain PCC7002, laying the foundation for improved transformation in this organism. MIJAMP is available athttps://code.ornl.gov/alexander-public/mijamp/.
Common marmosets use body posture as multi-functional signal to solicit, maintain, and modify social play
Authors: Adriaense Jessie E.C. , Ringen Erik J. , Ohashi Atsushi , Burkart Judith M. 
Published: August 2024

ABSTRACTSocial play is a highly active social interaction, characterized by rapid exchanges of various behaviors with multiple partners. Many primates use bodily expressions during social play, yet the potential signaling function of these expressions remains unclear. This study investigated whether common marmosets (Callithrix jacchus)use body posture as signal to regulate play. We recorded play within three captive common marmoset family groups using multiple cameras simultaneously to capture the fast-paced and high frequency behaviors. Three distinct signals (i.e. supine, hide, stalk) and six distinct play types (i.e. wrestle, chase, pounce, touch, catch, pull) were identified. We used a multi-state time-to-event model to analyze the sequences of play, including short-and long-term transitions between different states (i.e. signal, play, or rest/nothing). Our data-driven approach accounted for uncertainty in the duration of play bouts, using probabilistic classification rather than arbitrary bout thresholds. The resulting classifications allowed us to assess the social function of signals by comparing play behavior to a resting state baseline. We found that the presence of a signal: (1) increases the probability to play; (2) extends the duration of play; (3) leads to more diverse play; and (4) increases the probability of play fighting. Marmosets also show turn-taking of signaling and initiating subsequential play. These results show that marmosets use postures as communicative signals to initiate and change play dynamics, and thereby establish a mutual understanding of the joint action. The two-fold contribution of this study concerns novel analytical methods and a deeper conceptual understanding of primate communication. Play and its signals are important elements in the evolution of language, and our research contributes to its further understanding.
Navigating the Landscape of Fear
Authors: Gee Marissa , Gonzalez-Granda Nicolas , Joshi Sunay , Rudrapatna Nagaprasad , Somalwar Anne , Ellner Stephen P. , Vladimirsky Alexander 
Published: August 2024

AbstractAnimals searching for food must navigate through complex landscapes with varying terrain, food availability, predator activity, and shelter. One method for analyzing how foraging animals balance these competing interests is Optimal Foraging Theory, which posits that foragers make decisions that maximize some expected reward or utility. However, models have generally focused on simplified settings, especially regarding animal movement decisions, either ignoring spatial variability entirely or limiting the forager’s options to choosing among a few discrete habitat patches (or patch types) that are modeled as spatially uniform. In this paper, we present a model of optimal foraging in a continuous landscape for an animal that is subject to predation. Foraging animals thus must choose not only where to gather food, but also how to (safely) travel across the landscape. Furthermore, we explicitly model stochastic predator interactions, allowing us to predict optimal foraging trajectories conditional on the presence or absence of an immediate threat from a predator. We illustrate our model with numerical examples, one a hypothetical landscape with two regions of high food abundance and two areas of high predation risk on the direct route between the feeding areas and the forager’s overnight refuge, the other inspired by empirical data on foraging Samango monkeys (Cercopithecus albogularis schwarzi). We find that the shape of a forager’s utility function affects not only where it chooses to feed, but also the paths it takes to and from the optimal feeding ground. Thus, examining predicted optimal trajectories can provide additional information about what quantity, if any, animals optimize while foraging. We also develop and demonstrate a preliminary model for an animal that depletes the food supply in its local environment.
Quantifying the locality of the food supply in a large healthcare organisation
Authors: Utter Jennifer , Mole Frances , Johnston Henrietta , McCray Sally 
Published: August 2024

AbstractAimShocks to the food system (such as extreme weather events, wars, and pandemics) are felt by institutional food systems. For hospitals, these shocks affect the quantity, quality, and variety of foods that can be offered to patients. One strategy to buffer the hospital food supply from external threats is to prioritise ingredients produced locally. Thus, the aim of the current research is to describe the country of origin of all foods purchased by a large, metropolitan healthcare organisation and to identify opportunities for improving the locality of the food supply.MethodsThis study was of a cross‐sectional, observational design. The country of origin for all foods procured over a 1‐year period by a large, urban healthcare organisation was determined by proportion of food budget spend. State of origin was identified for fresh fruit, vegetables, and meat. The organisation was in Queensland, Australia and utilised a cook‐fresh, room‐service foodservice model. Descriptive analysis was used to to determine the number of items and the proportion of budget spend on all foods produced in Australia, and by food category. Similar descriptive statistics were generated to determine the proportion of the budget spend on fresh fruits, vegetables and meats produced in Queensland.ResultsOver the 1‐year period, 659 individual food items were purchased by the hospital foodservice, and 502 food items were included in the anlaysis. In total, 53% of the food budget was spent on Australian foods (100% Australian ingredients) and almost all fruit (73%) and vegetables (91%) were Australian grown. Procuring fresh fruit (28%), vegetables (35%), and meat (46%) from within the state was less common, and this may reflect the primary states of production across Australia, and seasonal variability of the food supply.ConclusionsFindings offer priority areas for improving the locality of the food supply. Future research to determine if procuring more foods locally has benefits to consistency of the food supply is warranted.
Blood–brain barrier dysfunction in aging is mediated by brain endothelial senescence
Authors: Novo João P. , Gee Lucy , Caetano Carolina A. , Tomé Inês , Vilaça Andreia , von Zglinicki Thomas , Moreira Irina S. , Jurk Diana , Rosa Susana , Ferreira Lino 
Published: August 2024

AbstractBBB dysfunction during aging is characterized by an increase in its permeability and phenotypic alterations of brain endothelial cells (BECs) including dysregulation of tight junction's expression. Here we have investigated the role of BEC senescence in the dysfunction of the BBB. Our results suggest that the transition from young to aged BBB is mediated, at least in part by BEC senescence.
Loss of immune cell identity with age inferred from large atlases of single cell transcriptomes
Authors: Connolly Erin , Pan Tony , Aluru Maneesha , Chockalingam Sriram , Dhere Vishal , Gibson Greg 
Published: August 2024

AbstractBy analyzing two large atlases of almost 4 million cells, we show that immune‐senescence involves a gradual loss of cellular identity, reflecting increased cellular heterogeneity, for effector, and cytotoxic immune cells. The effects are largely similar in both males and females and were robustly reproduced in two atlases, one assembled from 35 diverse studies including 678 adults, the other the OneK1K study of 982 adults. Since the mean transcriptional differences among cell‐types remain constant across age deciles, there is little evidence for the alternative mechanism of convergence of cell‐type identity. Key pathways promoting activation and stemness are down‐regulated in aged T cells, while CD8 TEM and CD4 CTLs exhibited elevated inflammatory, and cytotoxicity in older individuals. Elevated inflammatory signaling pathways, such as MAPK and TNF‐alpha signaling via NF‐kB, also occur across all aged immune cells, particularly amongst effector immune cells. This finding of lost transcriptional identity with age carries several implications, spanning from a fundamental biological understanding of aging mechanisms to clinical perspectives on the efficacy of immunomodulation in elderly people.
Using machine learning to explore the predictors of life satisfaction trajectories in older adults
Authors: Chen Honghui , Zhang Xueting , Bian Wenjun 
Published: August 2024

AbstractLife satisfaction is vital for older adults' well‐being, impacting various life aspects. It is dynamic, necessitating nuanced approaches to capture its trajectories accurately. This study aimed to explore the diverse trajectories and predictors of life satisfaction among older adults in China using longitudinal data from the China Health and Retirement Longitudinal Study. Latent class growth modeling and growth mixture modeling were employed to identify distinct trajectories of life satisfaction. Machine learning (ML) models were developed to predict different trajectories and identify important predictors of different trajectories. Four distinct trajectories of life satisfaction were identified, showcasing nuanced patterns of life satisfaction that changed over time. ML models, especially random forest, effectively predicted these trajectories. Emotional experiences (particularly the frequency of happiness and loneliness), body mass index, and self‐report health emerged as significant predictors of different life satisfaction trajectories. Our finding revealed the importance of focusing on individuals or groups with consistently low life satisfaction and paying more attention to mental and physical health predictors. Our models might guide future targeted preventative treatments.
International consensus definitions for infection‐triggered encephalopathy syndromes
Authors: Sakuma Hiroshi , Thomas Terrence , Debinski Carly , Eyre Michael , Han Velda X. , Jones Hannah F. , Kawano Go , Lee Vanessa W. , Malone Stephen , Matsuishi Toyojiro , Mohammad Shekeeb S. , Mori Takayuki , Nishida Hiroya , Nosadini Margherita , Takanashi Jun‐ichi , Mizuguchi Masashi , Lim Ming , Dale Russell C. 
Published: August 2024

AbstractAimTo develop standardized diagnostic criteria for ‘infection‐triggered encephalopathy syndrome (ITES)’ and five specific clinical syndromes of ITES.MethodThe draft definitions were based on existing criteria, standardized, and discussed by a panel of international experts using nominal group technique over 18 months to achieve consensus. All criteria use the same format: (1) presence of infection/fever; (2) clinical features including encephalopathy; (3) neuroradiological features on magnetic resonance imaging; (4) exclusion of other causes.ResultsWe first highlighted differences between ITES and infectious and autoimmune encephalitis, which is the most important differential diagnosis. Consensus was achieved to define five specific ITESs: acute encephalopathy with biphasic seizures and late reduced diffusion; acute necrotizing encephalopathy; mild encephalopathy with a reversible splenial lesion; acute fulminant cerebral oedema; and acute shock with encephalopathy and multiorgan failure. Two further conditions that are currently classified as epilepsy syndromes but have similar features to ITES, namely febrile infection‐related epilepsy syndrome and hemiconvulsion–hemiplegia–epilepsy syndrome, are also discussed.InterpretationThe consensus definition is expected to improve awareness of this disease concept, provide diagnostic framework, and facilitate future international research and clinical trials.