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    Genomic insights into the Montseny brook newt (Calotriton arnoldi), a Critically Endangered glacial relict

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    The Montseny brook newt (Calotriton arnoldi), considered the most endangered amphibian in Europe, is a relict salamandrid species endemic to a small massif located in northeastern Spain. Although conservation efforts should always be guided by genomic studies, those are yet scarce among urodeles, hampered by the extreme sizes of their genomes. Here, we present the third available genome assembly for the order Caudata, and the first genomic study of the species and its sister taxon, the Pyrenean brook newt (Calotriton asper), combining whole-genome and ddRADseq data. Our results reveal significant demographic oscillations which accurately mirrored Europe’s climatic history. Although severe bottlenecks have led to depauperate genomic diversity and long runs of homozygosity along a gigantic genome, inbreeding might have been avoided by assortative mating strategies. Other life history traits, however, seem to have been less advantageous, and the lack of land dispersal has driven to exceptional levels of population fragmentation.This article is published as Talavera, Adrián, Marc Palmada-Flores, Bernat Burriel-Carranza, Emilio Valbuena-Ureña, Gabriel Mochales-Riaño, Dean C. Adams, Héctor Tejero-Cicuéndez et al. "Genomic insights into the Montseny brook newt (Calotriton arnoldi), a Critically Endangered glacial relict." iScience 27 (2024): 108665. © 2023 The Authors.This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)

    Building Community: Supporting Minoritized Scholars through Library Publishing and Open and Equitable Revenue Models

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    With the growth of open access (OA) journal publishing, a myriad of funding models has emerged to serve as an alternative to the traditional subscription model. Models that impose author facing charges are inequitable, favoring well-resourced authors and institutions, and continue the dominance of publications from the Global North. This exploratory study critically examines the current state of funding OA journal publishing and the disruptive role of library publishing programs. We conclude with a discussion of the potential of the LYRASIS Open Access Community Investment Program as a tool to support library publishing programs to sustainably fund inclusive OA journal publishing.This article was originally published in College & Research Libraries 85, no. 1 (2024): 64-77. https://doi.org/10.5860/crl.85.1.64. The authors hold copyright and have licensed the article under a Creative Commons Attribution-NonCommercial 4.0 International License

    Development of doubled haploid inducer lines facilitates selection of superior haploid inducers in maize

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    Haploid inducers are key components of doubled haploid (DH) technology in maize. Robust agronomic performance and better haploid induction ability of inducers are persistently sought through genetic improvement. We herein developed C1-I inducers enabling large-scale in vivo haploid induction of inducers and discovered superior inducers from the DH progenies. The haploid induction rate (HIR) of C1-I inducers ranged between 5.8% and 12.0%. Overall, the success rate of DH production was 13% on average across the 23 different inducer crosses. The anthesis–silking interval and days to flowering of inducer F1s are significantly correlated with the success rate of DH production (r = −0.48 and 0.47, respectively). Transgressive segregants in DH inducers (DHIs) were found for the traits (days to flowering, HIR, plant height, and total primary branch length). Moreover, the best HIR in DHIs exceeded 23%. Parental genome contributions to DHI progenies ranged between 0.40 and 0.55, respectively, in 25 and 75 percentage quantiles, and the mean and median were 0.48. The allele frequency of the four traits from inducer parents to DHI progenies did not correspond with the phenotypic difference between superior and inferior individuals in the DH populations by genome-wide Fst analysis. This study demonstrated that the recombinant DHIs can be accessed on a large scale and used as materials to facilitate the genetic improvement of maternal haploid inducers by in vivo DH technology.This article is published as Chen Y-R, Lübberstedt T and Frei UK (2024) Development of doubled haploid inducer lines facilitates selection of superior haploid inducers in maize. Front. Plant Sci. 14:1320660. doi: 10.3389/fpls.2023.1320660.© 2024 Chen, Lübberstedt and Frei. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms

    Spirochaete genome identified in red abalone sample represents a novel genus Candidatus Haliotispira gen. nov. within the order Spirochaetales

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    A fully assembled spirochaete genome was identified as a contaminating scaffold in our red abalone (Haliotis rufescens) genome assembly. In this paper, we describe the analysis of this bacterial genome. The assembled spirochaete genome is 3.25 Mb in size with 48.5 mol% G+C content. The proteomes of 38 species were compared with the spirochaete genome and it was discovered to form an independent branch within the family Spirochaetaceae on the phylogenetic tree. The comparison of 16S rRNA sequences and average nucleotide identity scores between the spirochaete genome with known species of different families in Spirochaetia indicate that it is an unknown species. Further, the percentage of conserved proteins compared to neighbouring taxa confirm that it does not belong to a known genus within Spirochaetaceae. We propose the name Candidatus Haliotispira prima gen. nov., sp. nov. based on its taxonomic placement and origin. We also tested for the presence of this species in different species of abalone and found that it is also present in white abalone (Haliotis sorenseni). In addition, we highlight the need for better classification of taxa within the class Spirochaetia.This article is published as Sharma, Sharu Paul, Catherine M. Purcell, John R. Hyde, and Andrew J. Severin. "Spirochaete genome identified in red abalone sample represents a novel genus Candidatus Haliotispira gen. nov. within the order Spirochaetales." International Journal of Systematic and Evolutionary Microbiology 74, no. 1 (2024): 006198. doi: https://doi.org/10.1099/ijsem.0.006198. Copyright the authors, 2024. This is an open-access article distributed under the terms of the Creative Commons Attribution License

    Open Access Workflows for Academic Libraries

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    There is a growing acceptance of open access funding models among academic publishers, and a growing adoption of open access publishing agreements among academic libraries. In this context, libraries are taking on new roles and new processes to ensure the successful implementation of open access funding initiatives. This article will examine some of the key issues and considerations in the area of open access workflows, and discuss how one research-intensive library in the United States has approached these new functions.This is an accepted manuscript for an article that will be published in College and Research Libraries (July 2024), under a Creative Commons (CC BY-NC) License. Copyright 2023, The Authors

    Direct numerical simulation of electrokinetic transport phenomena in fluids: variational multi-scale stabilization and octree-based mesh refinement

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    Computational modeling of charged species transport has enabled the analysis, design, and optimization of a diverse array of electrochemical and electrokinetic devices. These systems are represented by the Poisson-Nernst-Planck (PNP) equations coupled with the Navier-Stokes (NS) equation. Direct numerical simulation (DNS) to accurately capture the spatio-temporal variation of ion concentration and current flux remains challenging due to the (a) small critical dimension of the diffuse charge layer (DCL), (b) stiff coupling due to fast charge relaxation times, large advective effects, and steep gradients close to boundaries, and (c) complex geometries exhibited by electrochemical devices. In the current study, we address these challenges by presenting a direct numerical simulation framework that incorporates (a) a variational multiscale (VMS) treatment, (b) a block-iterative strategy in conjunction with semi-implicit (for NS) and implicit (for PNP) time integrators, and (c) octree based adaptive mesh refinement. The VMS formulation provides numerical stabilization critical for capturing the electro-convective flows often observed in engineered devices. The block-iterative strategy decouples the difficulty of non-linear coupling between the NS and PNP equations and allows the use of tailored numerical schemes separately for NS and PNP equations. The carefully designed second-order, hybrid implicit methods circumvent the harsh timestep requirements of explicit time steppers, thus enabling simulations over longer time horizons. Finally, the octree-based meshing allows efficient and targeted spatial resolution of the DCL. These features are incorporated into a massively parallel computational framework, enabling the simulation of realistic engineering electrochemical devices. The numerical framework is illustrated using several challenging canonical examples.This is a preprint from Kim, Sungu, Kumar Saurabh, Makrand A. Khanwale, Ali Mani, Robbyn K. Anand, and Baskar Ganapathysubramanian. "Direct numerical simulation of electrokinetic transport phenomena: variational multi-scale stabilization and octree-based mesh refinement." arXiv preprint arXiv:2301.05985 (2023). doi: https://doi.org/10.48550/arXiv.2301.05985. Copyright the authors 2024. CC BY

    Leveraging Soil Mapping and Machine Learning to Improve Spatial Adjustments in Plant Breeding Trials

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    Spatial adjustments are used to improve the estimate of plot seed yield across crops and geographies. Moving mean and P-Spline are examples of spatial adjustment methods used in plant breeding trials to deal with field heterogeneity. Within trial spatial variability primarily comes from soil feature gradients, such as nutrients, but study of the importance of various soil factors including nutrients is lacking. We analyzed plant breeding progeny row and preliminary yield trial data of a public soybean breeding program across three years consisting of 43,545 plots. We compared several spatial adjustment methods: unadjusted (as a control), moving means adjustment, P-spline adjustment, and a machine learning based method called XGBoost. XGBoost modeled soil features at (a) local field scale for each generation and per year, and (b) all inclusive field scale spanning all generations and years. We report the usefulness of spatial adjustments at both progeny row and preliminary yield trial stages of field testing, and additionally provide ways to utilize interpretability insights of soil features in spatial adjustments. These results empower breeders to further refine selection criteria to make more accurate selections, and furthermore include soil variables to select for macro– and micro-nutrients stress tolerance.This is a preprint from Carroll, Matthew E., Luis G. Riera, Bradley A. Miller, Philip M. Dixon, Baskar Ganapathysubramanian, Soumik Sarkar, and Asheesh K. Singh. "Leveraging Soil Mapping and Machine Learning to Improve Spatial Adjustments in Plant Breeding Trials." bioRxiv (2024): 2024-01. doi: https://doi.org/10.1101/2024.01.03.574114. The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license

    Continuous cropping of potato changed the metabolic pathway of root exudates to drive rhizosphere microflora

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    For potato production, continuous cropping (CC) could lead to autotoxicity buildup and microflora imbalance in the field soil, which may result in failure of crops and reduction in yield. In this study, non-targeted metabolomics (via liquid chromatography with tandem mass spectrometry (LC–MS/MS)) combined with metagenomic profiling (via high-throughput amplicon sequencing) were used to evaluate correlations between metabolomics of potato root exudates and communities of bacteria and fungi around potato plants to illustrate the impacts of CC. Potato plants were grown in soil collected from fields with various CC years (0, 1, 4, and 7 years). Metabolomic analysis showed that the contents and types of potential autotoxins in potato root exudates increased significantly in CC4 and CC7 plants (i.e., grown in soils with 4 and 7 years of CC). The differentially expressed metabolites were mainly produced via alpha-linolenic acid metabolism in plant groups CC0 and CC1 (i.e., no CC or 1 year CC). The metabolomics of the groups CC4 and CC7 became dominated by styrene degradation, biosynthesis of siderophore group non-ribosomal peptides, phenylpropanoid biosynthesis, and biosynthesis of various plant secondary metabolites. Continuous cropping beyond 4 years significantly changed the bacterial and fungal communities in the soil around the potato crops, with significant reduction of beneficial bacteria and accumulation of harmful fungi. Correlations between DEMs and microflora biomarkers were established with strong significances. These results suggested that continuous cropping of potato crops changed their metabolism as reflected in the plant root exudates and drove rhizosphere microflora to directions less favorable to plant growth, and it needs to be well managed to assure potato yield.This article is published as Xing, Yanhong, Pingliang Zhang, Wenming Zhang, Chenxu Yu, and Zhuzhu Luo. "Continuous cropping of potato changed the metabolic pathway of root exudates to drive rhizosphere microflora." Frontiers in Microbiology 14: 1318586. doi: https://doi.org/10.3389/fmicb.2023.1318586. © 2024 Xing, Zhang, Zhang, Yu and Luo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY)

    Understanding intentionally and non-intentionally added substances and associated threshold of toxicological concern in post-consumer polyolefin for use as food packaging materials

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    The use of post-consumer recycled (PCR) polymers in food contact materials (FCMs) can facilitate achieving a circular economy by reducing environmental waste and landfill accumulation. This study aimed to identify potentially harmful substances, including non-intentionally added substances (NIAS) and unapproved intentionally added substances (IAS), in polyolefin samples from material recovery facilities using gas-chromatography mass-spectrometry. Selected phthalates and bisphenols were quantified by targeted gas-chromatography tandem mass-spectrometry. The analysis detected 9 compounds in virgin polymers and 52 different compounds including alcohols, hydrocarbons, phenols in virgin and hydrocarbons, aromatic, phthalates, organic acids, per- and polyfluoroalkyl substances (PFAS) in PCR polymers. The Cramer classification system was used to assesses the Threshold of Toxicological Concern associated with the detected compounds. The PCR sample showed a slightly higher proportion of Cramer Class III compounds (48.08 %) than the virgin sample (44.44 %), indicating higher toxicity potential. Quantification detected bisphenols only in PCR material including BPA (2.88 ± 0.53 μg/g), BPS (5.12 ± 0.003 μg/g), BPF (3.42 ± 0.01 μg/g), and BADGE (4.638 μg/g). Phthalate concentrations were higher in PCR than virgin samples, with the highest levels detected as DIDP, at 6.18 ± 0.31 μg/g for PCR and 6.04 ± 0.02 for virgin. This study provides critical understanding of the safety and potential risks associated with using PCR polyolefins from different sources in food contact applications.This article is published as Tumu, K.,Vorst,K., Curtzwiler, G., Understanding intentionally and non-intentionally added substances and associated threshold of toxicological concern in post-consumer polyolefin for use as food packaging materials. Heliyon. January 15 2024, Early View; e23620.https://doi.org/10.1016/j.heliyon.2023.e23620. Posted with permission. This article is available under the Creative Commons CC-BY-NC-ND license and permits non-commercial use of the work as published, without adaptation or alteration provided the work is fully attributed

    Why Are People Duped by Health Disinformation Campaigns?

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    Health disinformation campaigns pose a serious threat to societal well-being. To better understand how these campaigns are propagated, this research evaluates how successful people are at identifying false health-related content. Using a survey methodology, a sample of 71 university students was asked to review 10 pairs of social media posts and determine their veracity. Mixed models were used to analyze successful detection of disinformation. Factors that affected participants’ judgements were qualitatively assessed. Participants demonstrated a 90% success rate when differentiating between true and false posts, indicating a high level of success when confronted with a choice between two posts. Commonly used indicators of honest and dishonest content were also identified. These insights offer a nuanced understanding of social media users’ evaluations of online content and can inform mitigation strategies designed to combat health disinformation campaigns.This presentation is published as George, J.F., Mannina, S., Why Are People Duped by Health Disinformation Campaigns? Presented at Proceedings of the 57th Hawaii International Conference on System Sciences, 2024. URI: https://hdl.handle.net/10125/106392 978-0-9981331-7-1. Posted with permission. (CC BY-NC-ND 4.0

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