bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do macroinvertebrate abundance and community structure depend on the quality of ponds located in peri-urban areas?
Authors: Hulot Florence D. , Hanot Christophe , Nélieu Sylvie , Lamy Isabelle , Karolak Sara , Delarue Ghislaine , Baudry Emmanuelle 
Published: October 2023

AbstractContamination is one of the major threats to freshwater biodiversity. Compared to other aquatic ecosystems, peri-urban ponds are unique because they are embedded in human-dominated areas. However, it is poorly understood how different land uses such as urban or agricultural contribute multiple pollutants to ponds and thus affect pond biodiversity. In this work, 12 ponds located in a peri-urban area (Ile-de-France region, France) were monitored for 2 consecutive years in spring and fall. We surveyed macroinvertebrates and measured the physicochemical parameters and contaminants of different classes (trace elements, pharmaceuticals, pesticides and polycyclic aromatic hydrocarbons) in both water and sediment. The objective was twofold: (1) to explore local and regional macroinvertebrate spatiotemporal diversity and (2) to understand the effects of contaminants on community structure. We observed 236 macroinvertebrate morphotaxa, none of which were rare or sensitive to pollutants. Morphotaxa richness showed small differences between ponds but no difference between there was no effect of field campaign. There was no effect of ponds and field campaign on morphotaxa diversity and equitability. We did not observe a relationship between land use around the pond (agricultural, urban, or semi-natural) and diversity indices with the exception of the proportion of agricultural land in the vicinity of the pond on equitability. Regional beta diversity (between ponds) showed that differences in morphotaxa composition reflected species replacement more than differences in species richness; these were primarily due to the high abundance of pollutant-tolerant species in some of the ponds. The effects of environmental parameters on community structure were studied using partial redundancy analysis based on the presence-absence of morphotaxa, showing that community assemblages are shaped by sediment levels of pharmaceuticals, water conductivity and ammonium concentration. In conclusion, ponds in peri-urban areas are exposed to various human activities, with our results suggesting that this exposure leads to chronic and diverse contaminations that affect morphotaxa communities.
Genome of the glacier algaAncylonemaand its insights into the evolution of streptophyte life on ice and land
Authors: Bowles Alexander M. C. , Williams Tom A. , Donoghue Philip C. J. , Campbell Douglas A. , Williamson Christopher J. 
Published: October 2023

AbstractContemporary glaciers and ice sheets are home to communities of streptophyte glacier algae that must balance their requirements for photosynthesis and growth with tolerance of extremes in temperature, desiccation and UV radiation. These same environmental challenges have been hypothesized as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720–635 million years ago). Here, we sequence, assemble and analyze the metagenome-assembled genome (MAG) of the glacier algaAncylonema nordenskiöldiito investigate its adaptations to life in ice, and whether this represents a vestige of Cryogenian anydrophyte exaptations. Phylogenetic analysis confirms the placement of glacier algae within the sister lineage to land plants, Zygnematophyceae. The MAG is characterized by an expansion of genes involved in high irradiance and UV light tolerance, whilst lineage-specific diversification led to the novel screening pigmentation of glacier algae. We found no support for the hypothesis of a common genomic basis for adaptations to ice and to land in streptophytes. Comparative genomic analysis revealed that reductive genome evolution in the ancestor of Zygnematophyceae correlates with their reductive morphological evolution. This first genome-scale data for glacier algae supports anAncylonema-specific adaptation to the cryosphere, as well as shedding light on the genome evolution of land plants and Zygnematophyceae.
Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility
Authors: Kommu Navya , Stothard Paul , Chukwujindu Christian , Pathak Ashish , Chauhan Ashvini 
Published: October 2023

AbstractShotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements in bioinformatic techniques, it is now possible to in-silico retrieve sequences that belong to specific taxa, followed by assembly and annotation and the obtained sequences are called as metagenome-assembled genome (MAG), which facilitates better understanding of metabolic and other traits without having to culture the microorganism. We applied the MAG technique using the nf-core/mag pipeline on shotgun metagenome sequences obtained from a soil ecosystem that has long-term co-contamination with radionuclides (mainly uranium), heavy metals (mercury, nickel etc.) and organic compounds. Annotation of MAGs was performed using SPAdes and MEGAHIT and genomes were binned and taxonomically classified using the GTDBTk and CAT toolkits within nf-core/mag. Additional annotations were done using Prokka and Prodigal and the dRep program was used to choose specific MAGs for further analysis. Initial analysis resulted in a total of 254 MAGs which met the high-quality standard with the completeness > 95% and contamination < 5%, accounting for 26.67% of all the MAGs (Fig SI-1). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Summer season) were reconstructed. These 27 MAGs span across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Overall, theArthrobacterMAG was found to be one that was robust for further analysis. Over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorous, sulfur and 598 genes encoding enzymes for metals resistance from cadmium, zinc, chromium, arsenic and copper. In summary, this project enhances our understanding of genes conferring resistance to heavy metals in uranium contaminated soils.
A homeostatic gut-to-brain insulin antagonist restrains neuronally stimulated fat loss
Authors: Liu Chung-Chih , Khan Ayub , Seban Nicholas , Littlejohn Nicole , Srinivasan Supriya 
Published: October 2023

ABSTRACTInC. elegansmechanisms by which peripheral organs relay internal state information to the nervous system remain unknown, although strong evidence suggests that such signals do exist. Here we report the discovery of a peptide of the ancestral insulin superfamily called INS-7 that functions as an enteroendocrine peptide and is secreted from specialized cells of the intestine. INS-7 secretion increases during fasting, and acts as a bona fide gut-to-brain homeostatic signal that attenuates neuronally induced fat loss during food shortage. INS-7 functions as an antagonist at the canonical DAF-2 receptor in the nervous system, and phylogenetic analysis suggests that INS-7 bears greater resemblance to members of the broad insulin/relaxin superfamily than to conventional mammalian insulin and IGF peptides. The discovery of an endogenous insulin antagonist secreted by specialized intestinal cell with enteroendocrine functions suggests that much remains to be learned about the intestine and its role in directing neuronal functions.
Combining Blood-Based Biomarkers and Structural MRI Measurements to Distinguish Persons With and Without Significant Amyloid Plaques
Authors: Chen Yanxi , Su Yi , Wu Jianfeng , Chen Kewei , Atri Alireza , Caselli Richard J , Reiman Eric M. , Wang Yalin ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: October 2023

ABSTRACTBackgroundAmyloid-β (Aβ) plaques play a pivotal role in Alzheimer’s disease. The current positron emission tomography (PET) is expensive and limited in availability. In contrast, blood-based biomarkers (BBBMs) show potential for characterizing Aβ plaques more affordably. We have previously proposed an MRI-based hippocampal morphometry measure to be an indicator of Aβ-plaques.ObjectiveTo develop and validate an integrated model to predict brain amyloid PET positivity combining MRI feature and plasma Aβ42/40 ratio.MethodsWe extracted hippocampal multivariate morphometry statistics (MMS) from MR images and together with plasma Aβ42/40 trained a random forest classifier to perform a binary classification of participant brain amyloid PET positivity. We evaluated the model performance using two distinct cohorts, one from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the other from the Banner Alzheimer’s Institute (BAI), including prediction accuracy, precision, recall rate, F1 score and AUC score.ResultsResults from ADNI (mean age 72.6, Aβ+ rate 49.5%) and BAI (mean age 66.2, Aβ+ rate 36.9%) datasets revealed the integrated multimodal (IMM) model’s superior performance over unimodal models. The IMM model achieved prediction accuracies of 0.86 in ADNI and 0.92 in BAI, surpassing unimodal models based solely on structural MRI (0.81 and 0.87) or plasma Aβ42/40 (0.73 and 0.81) predictors.ConclusionOur IMM model, combining MRI and BBBM data, offers a highly accurate approach to predict brain amyloid PET positivity. This innovative multiplex biomarker strategy presents an accessible and cost-effective avenue for advancing Alzheimer’s disease diagnostics, leveraging diverse pathologic features related to Aβ plaques and structural MRI.
Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer
Authors: Blise Katie E. , Sivagnanam Shamilene , Betts Courtney B. , Betre Konjit , Kirchberger Nell , Tate Benjamin , Furth Emma E. , Dias Costa Andressa , Nowak Jonathan A. , Wolpin Brian M. , Vonderheide Robert H. , Goecks Jeremy , Coussens Lisa M. , Byrne Katelyn T. 
Published: October 2023

ABSTRACTTumor molecular datasets are becoming increasingly complex, making it nearly impossible for humans alone to effectively analyze them. Here, we demonstrate the power of using machine learning to analyze a single-cell, spatial, and highly multiplexed proteomic dataset from human pancreatic cancer and reveal underlying biological mechanisms that may contribute to clinical outcome. A novel multiplex immunohistochemistry antibody panel was used to audit T cell functionality and spatial localization in resected tumors from treatment-naive patients with localized pancreatic ductal adenocarcinoma (PDAC) compared to a second cohort of patients treated with neoadjuvant agonistic CD40 (αCD40) monoclonal antibody therapy. In total, nearly 2.5 million cells from 306 tissue regions collected from 29 patients across both treatment cohorts were assayed, and more than 1,000 tumor microenvironment (TME) features were quantified. We then trained machine learning models to accurately predict αCD40 treatment status and disease-free survival (DFS) following αCD40 therapy based upon TME features. Through downstream interpretation of the machine learning models’ predictions, we found αCD40 therapy to reduce canonical aspects of T cell exhaustion within the TME, as compared to treatment-naive TMEs. Using automated clustering approaches, we found improved DFS following αCD40 therapy to correlate with the increased presence of CD44+CD4+Th1 cells located specifically within cellular spatial neighborhoods characterized by increased T cell proliferation, antigen-experience, and cytotoxicity in immune aggregates. Overall, our results demonstrate the utility of machine learning in molecular cancer immunology applications, highlight the impact of αCD40 therapy on T cells within the TME, and identify potential candidate biomarkers of DFS for αCD40-treated patients with PDAC.
From disturbances to nonlinear fitness and back
Authors: Tuljapurkar Shripad , Jaggi Harman , Gascoigne Samuel J. L. , Zuo Wenyun , Kajin Maja , Salguero-Gómez Roberto 
Published: October 2023

AbstractA fundamental goal of Ecology is to predict how natural populations respond to disturbances. Accordingly, the last decades have witnessed key theoretical developments in stochastic demography and transient dynamics. However, both areas, have to date been largely disconnected. Here, we introduce an expression for the second derivatives of population growth rate with respect to demographic rates (e.g. survival-dependent state transitions and reproduction) with direct links to transient dynamics. We use this connection to develop a new mathematical framework showing how transient responses to pulse disturbances lead to a quantitative description of press disturbances. Second-derivatives of population growth rate with respect to said demographic rates are valuable as they quantify the degree of nonlinear selection acting on demographic rates and how environments shape the long-term performance of populations. Whilst valuable, previous methods to quantify second-order derivatives have heavily relied on vector calculus-potentially obscuring important demographic processes connected to second-order derivatives. Here we offer an intuitive method using perturbation theory and our approach is valid for any discrete-time, st(age)-based structured population model. Importantly, our new method implicates an intimate relationship between the nonlinear selection pressures acting on demographic rates with the emergent transient dynamics of populations over time. We showcase these relationships through mathematical proofs, connecting to Cohen’s cumulative distance, and identifying a strong relationship between generation time across 439 unique plant and animal species (2690 population models). As such, this new method represents a valuable tool for population ecologists, comparative demographers, and conservation biologists to understand and protect structured populations in a changing world.
A systematic screen for co-option of transposable elements across the fungal kingdom
Authors: Oggenfuss Ursula , Badet Thomas , Croll Daniel 
Published: October 2023

AbstractHow novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1,237 genomes spanning the phylogenetic breadth of the fungal kingdom. We scanned proteomes for evidence of co-occurrence of TE-derived domains along with other conventional protein functional domains. We detected more than 13,000 predicted proteins containing potentially TE-derived domain, of which 825 were identified in more than five genomes, indicating that many host-TE fusions may have persisted over long evolutionary time scales. We used the phylogenetic context to identify the origin and retention of individual TE-derived domains. The most common TE-derived domains are helicases derived fromAcadem,KolobokorHelitron.We found putative TE co-options at a higher rate in genomes of the Saccharomycotina, providing an unexpected source of protein novelty in these generally TE depleted genomes. We investigated in detail a candidate host-TE fusion with a heterochromatic transcriptional silencing function that may play a role in TE and gene regulation in ascomycetes. The affected gene underwent multiple full or partial losses within the phylum. Overall, our work establishes a kingdom-wide view of how domains likely derived from TEs contribute to the evolution of protein functions.
Integrated Proteomics Identifies Troponin I Isoform Switch as a Regulator of a Sarcomere-Metabolism Axis During Cardiac Regeneration
Authors: Aballo Timothy J. , Bae Jiyoung , Paltzer Wyatt G. , Chapman Emily A. , Salamon Rebecca J. , Mann Morgan M. , Ge Ying , Mahmoud Ahmed I. 
Published: October 2023

ABSTRACTAdult mammalian cardiomyocytes have limited proliferative potential, and after myocardial infarction (MI), injured cardiac tissue is replaced with fibrotic scar rather than with functioning myocardium. In contrast, the neonatal mouse heart possesses a regenerative capacity governed by cardiomyocyte proliferation; however, a metabolic switch from glycolysis to fatty acid oxidation during postnatal development results in loss of this regenerative capacity. Interestingly, a sarcomere isoform switch also takes place during postnatal development where slow skeletal troponin I (ssTnI) is replaced with cardiac troponin I (cTnI). In this study, we first employ integrated quantitative bottom-up and top-down proteomics to comprehensively define the proteomic and sarcomeric landscape during postnatal heart maturation. Utilizing a cardiomyocyte-specific ssTnI transgenic mouse model, we found that ssTnI overexpression increased cardiomyocyte proliferation and the cardiac regenerative capacity of the postnatal heart following MI compared to control mice by histological analysis. Our global proteomic analysis of ssTnI transgenic mice following MI reveals that ssTnI overexpression induces a significant shift in the cardiac proteomic landscape. This shift is characterized by an upregulation of key proteins involved in glycolytic metabolism. Collectively, our data suggest that the postnatal TnI isoform switch may play a role in the metabolic shift from glycolysis to fatty acid oxidation during postnatal maturation. This underscores the significance of a sarcomere-metabolism axis during cardiomyocyte proliferation and heart regeneration.
Bio-efficacy of field aged novel class of long-lasting insecticidal nets, against pyrethroid-resistant malaria vectors in Tanzania: A series of experimental hut trials
Authors: Martin Jackline L. , Messenger Louisa A. , Rowland Mark , Mosha Franklin W , Bernard Edmund , Kisamo Monica , Limbe Shaban , Hape Patric , Thickstun Charles , Steven Crene , Moshi Oliva , Shirima Boniface , Matowo Nancy S. , Mosha Jacklin F , Dee Dominic P , Churcher Thomas S , Kulkarni Manisha A. , Manjurano Alphaxard , Protopopoff Natacha 
Published: October 2023

AbstractNew classes of long-lasting insecticidal nets (LLINs) incorporating two insecticides, or an insecticide and a synergist, are recommended by the World Health Organization (WHO) to prevent malaria transmitted by mosquito vectors resistant to pyrethroid and other common insecticide classes. This study was nested in a large-scale cluster-randomized controlled trial conducted in Tanzania. A series of experimental hut trials (EHTs) aimed to evaluate the bio-efficacy of trial LLINs on the mosquito indicators most pertinent to malaria transmission over 3 years of use in the community. The aim was to evaluate nets subjected to a broader range of household factors than WHO standardized washing.The following field collected LLINs were assessed: 1/OlysetTMPlus (combining piperonyl butoxide synergist and permethrin), 2/Interceptor®G2 (chlorfenapyr and alpha-cypermethrin), 3/Royal Guard®(pyriproxyfen and alpha-cypermethrin), 4/Interceptor®(alpha-cypermethrin only), 5/a new Interceptor®, and 6/an untreated net. Thirty nets of each type were withdrawn from the community at 12, 24 and 36 months after distribution and used for the EHTs. Pre-specified outcomes were 72-hour mortality for Interceptor®G2, 24-hour mortality for OlysetTMPlus, and fertility based on egg development stage for Royal Guard®.Overall; Interceptor®G2 LLINs induced higher 72-hour mortality compared to standard LLINs of the same age up to 12 months (44% vs 21%), OR: 3.5, 95% CI: 1.9 – 6.6, p-value < 0.001 and 24-hour mortality was only significantly higher in OlysetTMPlus when new (OR: 13.6, 95%CI: 4.4 – 41.3, p-value < 0.001) compared to standard LLINs but not at 12 months (17% vs 13%; OR: 2.1, 95% CI: 1.0 – 4.3; p-value = 0.112). A small non-significant effect of pyriproxyfen onAnophelesfertility was observed for Royal Guard®up to 12 months (75% vs 98%, OR: 1.1, 95% CI: 0.0 – 24.9, p-value = 0.951). There was no evidence of a difference in the main outcomes for any of the new class of LLINs at 24 and 36 months compared to standard LLINs.Interceptor®G2 LLINs showed superior bio-efficacy compared to standard LLINs for only up to 12 months and the effect of OlysetTMPlus was observed when new for all species and 12 months forAn. gambiaes.l. only. The pyriproxyfen component of Royal Guard®had a short and limited effect on fertility
Evidence for a role of synchrony but not common fate in the perception of biological group movements
Authors: Cracco Emiel , Papeo Liuba , Wiersema Jan R. 
Published: October 2023

AbstractExtensive research has shown that observers are able to efficiently extract summary information from groups of people. However, little is known about the cues that determine whether multiple people are represented as a social group or as independent individuals. Initial research on this topic has primarily focused on the role of static cues. Here, we instead investigate the role of dynamic cues. In two experiments with male and female human participants, we use EEG frequency tagging to investigate the influence of two fundamental Gestalt principles - synchrony and common fate - on the grouping of biological movements. In Experiment 1, we find that brain responses coupled to four point-light figures walking together are enhanced when they move in sync vs. out of sync, but only when they are presented upright. In contrast, we found no effect of movement direction (i.e., common fate). In Experiment 2, we rule out that synchrony takes precedence over common fate by replicating the null effect of movement direction while keeping synchrony. These results put forward synchrony as an important driver of social grouping, consistent with the fact that it is an important feature of social interaction and an indicator of social cohesion. In contrast, the influence of common fate on social grouping is less clear and will require further research.
A continental-scale analysis reveals the latitudinal gradient of stomatal density across amphistomatous species: Evolutionary history vs. present-day environment
Authors: Liu Congcong , Huang Kexiang , Zhao Yifei , Li Ying , He Nianpeng 
Published: October 2023

AbstractAmphistomy is a potential method for increasing photosynthetic rate; however, latitudinal gradients of stomatal density across amphistomatous species and their drivers remain unknown. Here, the adaxial stomatal density (SDad) and abaxial stomatal density (SDab) of 486 amphistomatous species-site combinations, belonging to 32 plant families, were collected from China, and their total stomatal density (SDtotal) and stomatal ratio (SR) were calculated. Overall, these four stomatal traits did not show significant phylogenetic signals. There were no significant differences in SDaband SDtotalbetween woody and herbaceous species, but SDadand SR were higher in woody species than in herbaceous species. Besides, a significantly positive relationship between SDaband SDadwas observed. We also found that stomatal density (including SDab, SDad, and SDtotal) decreased with latitude while SR increased with latitude, and temperature seasonality was the most important environmental factor driving it. Besides, evolutionary history (represented by both phylogeny and species) explained about 10–22 fold more of the variation in stomatal traits than the present-day environment (65.2%–71.1% vs. 2.9%–6.8%). Our study extended our knowledge of trait-environment relationships and highlighted the importance of evolutionary history in driving stomatal trait variability.