bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustainability of seed harvesting in wild plant populations: an insight from a global database of matrix population models
Authors: Bucharova Anna , Bossdorf Oliver , Scheepens J. F. , Salguero-Gómez Roberto 
Published: January 2023

AbstractSeed harvesting from wild plant populations is key for ecological restoration, but may threaten the persistence of source populations. Consequently, several countries have set guidelines limiting the proportions of harvestable seeds. However, these guidelines are so far inconsistent, and they lack a solid empirical basis. Here, we use high-resolution data from 298 plant species to model the demographic consequences of seed harvesting. We find that the current guidelines do not protect populations of annuals and short-lived perennials, while they are overly restrictive for long-lived plants. We show that the maximum possible fraction of seed production – what can be harvested without compromising the long-term persistence of populations – is strongly related to the generation time of the target species. When harvesting every year, this safe seed fraction ranges from 80% in long-lived species to 2% in most annuals. Less frequent seed harvesting substantially increases the safe seed fraction: In the most vulnerable annual species, it is safe to harvest 5%, 10% or 30% of population seed production when harvesting every two, five or ten years, respectively. Our results provide a quantitative basis for seed harvesting legislations worldwide, based on species’ generation time and harvesting regime.SignificanceThe UN Decade on Ecosystem Restoration, 2021-2030, foresees upscaling restoration, and the demand for native seed is skyrocketing. Seeds for restoring native vegetation are often harvested in wild, but too intensive harvest can threaten the donor populations. Existing guidelines that set limits to wild seed harvest are mostly based on expert opinions, yet they commonly lack empirical basis and vary among regions in one order of magnitude. We show that the current guidelines urgently need to be reformulated, because they are overly restrictive in long-lived species, while they do not protect annual plants from extinction. Using matrix population models of nearly 300 plant species, we provide a quantitative basis for a new seed harvesting legislation world-wide.
Knowledge “installed” diffusion model predicts the geometry of actin cytoskeleton from cell morphology
Authors: Li Honghan , Liu Shiyou , Deguchi Shinji , Matsunaga Daiki 
Published: January 2023

AbstractCells exhibit various morphological characteristics due to their physiological activities, and changes in cell morphology are inherently accompanied by the assembly and disassembly of the actin cytoskeleton. Stress fibers are a prominent component of the actin-based intracellular structure and are highly involved in numerous physiological processes, e.g., mechanotransduction and maintenance of cell morphology. Although it is widely accepted that variations in cell geometry interact with the distribution and localization of stress fibers, it remains unclear if there are underlying geometric principles between the cell morphology and actin cytoskeleton. Here we present a machine learning system, which uses the diffusion model, that can convert the cell shape to the distribution of stress fibers. By training with corresponding datasets of cell shape and stress fibers, our system learns the conversion to generate the stress fiber images from its corresponding cell shape. The predicted stress fiber distribution has good agreement with the experimental data, and the overlap region of predicted and experimentally observed stress fibers reaches 79.3 ±12.4%. We then found some unknown natures such as a linear relation relationship between the stress fiber length and cell area. With this “installed” conversion relation between cellular morphology and corresponding stress fibers’ localization, our system could perform virtual experiments that provide a visual map showing the probability of stress fiber distribution from the virtual cell shape. Our system provides a powerful approach to seek further hidden geometric principles between the cell morphologies and actin cytoskeletons.
Between a rock and a hard place: Effects of land-use change on rock-dwelling animals of lateritic plateaus in the northern Western Ghats
Authors: Jithin Vijayan , Rane Manali , Watve Aparna , Giri Varad B. , Naniwadekar Rohit 
Published: January 2023

ABSTRACTOpen natural ecosystems like lateritic plateaus, are undergoing rapid transformation with very poor understanding of these impacts on the threatened and endemic biodiversity. The unprotected, low-elevation lateritic plateaus of the northern Western Ghats are case to the point, as they have high endemicity but remain unprotected under Indian law. We aimed to understand the impact of the conversion of the natural lateritic plateaus to agroforestry and paddy cultivation on biodiversity. We compared the prevalence of two species of endemic herpetofauna of the northern Western Ghats (Gegeneophis seschachariandHemidactylus albofasciatus) and a widespread snake (Echis carinatus) and the composition of other rock-dwelling animals across 12 undisturbed plateau sites and 10 sites each in agroforestry plantations and abandoned paddies on plateaus using time-constrained searches. We had 5738 encounters with 38 different animal species/groups. We found that the abundance of large rocks, which were the most-preferred size class of rocks by animals, was higher in abandoned paddy compared to plateaus and orchards. However, the prevalence ofH. albofasciatusandE. carinatuswas highest on undisturbed plateaus. Contrastingly, the prevalence ofG. seshachariwas significantly higher in abandoned paddy than undisturbed plateau or orchards. Non-metric multi-dimensional analysis showed that the assemblage of rock-dwelling fauna differed significantly across the three land-use types. Despite being adapted to persist in extremely variable climates on lateritic plateaus, we find that multiple species/groups are vulnerable to land-use change. However,G. seshachariand a few other taxa appear to benefit from certain kinds of land-use change, highlighting the context-specificity in species responses. While multiple studies have determined the impacts of forest conversion to other land-uses, this is one of the first studies to determine the impacts of the conversion of rocky outcrops, thereby highlighting the conservation value of habitats that are often classified as wastelands.
Reverse chemical ecology approach for sustainable palm tree protection against invasive palm weevils
Authors: Antony Binu , Montagné Nicolas , Comte Arthur , Mfarrej Sara , Jakše Jernej , Capoduro Rémi , Shelke Rajan , Cali Khasim , AlSaleh Mohammed Ali , Persaud Krishna , Pain Arnab , Jacquin-Joly Emmanuelle 
Published: January 2023

AbstractThe reverse chemical ecology approach facilitates sustainable plant protection by identifying odorant receptors (ORs) tuned to odorants, especially the volatile molecules emitted from host plants that insects use for detection. A few studies have explored such an approach to develop sustainable pest management programs, especially in host-specialized insect species. We revealed the molecular mechanism of host plant detection of a destructive, invasive insect pest of palm trees (Arecaceae), the Asian palm weevil (Rhynchophorus ferrugineus), by deorphanizing an OR (RferOR2) tuned to several palm-emitted odors. We found that RferOR2 responded explicitly to several ecologically relevant palm-emitted odors and significantly to palm esters when transgenically expressed inDrosophilaolfactory neurons. We mapped RferOR2 expression in theR. ferrugineusgenome and found that odor specificity is likely to develop equally in both sexes. We inferred that the semiochemicals that attract palm weevils to a palm tree might aid in weevil control efforts by improving attraction, enticing many palm weevils to the traps. We demonstrate that including synthetic palm volatiles in pheromone-based mass trapping has a synergistic effect on pheromones, resulting in significantly increased weevil catches. We proved that insect OR deorphanization could aid in the identification of novel behaviorally active volatiles for inclusion in pest management. These results suggest that targeting RferOR2 may help design receptor antagonists that can interfere with weevil host-searching behavior in sustainable pest management applications.SignificanceAsian and South American palm weevils are tremendously important agricultural pests primarily adapted to palm trees and cause severe destruction, threatening sustainable palm cultivation worldwide. The host plant selection of these weevils is mainly attributed to functional specialization of odorant receptors that detect palm-derived volatiles. We unraveled the intricacies of weevil–palm tree communication by deorphanizing an odorant receptor tuned to natural palm-emitted odors. We used palm ester volatiles, which produced a significant response in the functional studies, and proved their synergistic effect on the pheromone coinciding with increased weevil catches in the field. We revealed that insect odorant receptor deorphanization could help identify novel behaviorally active volatiles (reverse chemical ecology) for sustainable palm protection.
An Open-Source Platform for Head-Fixed Operant and Consummatory Behavior
Authors: Gordon-Fennell Adam , Barbakh Joumana M. , Utley MacKenzie , Singh Shreya , Bazzino Paula , Gowrishankar Raajaram , Bruchas Michael R. , Roitman Mitchell F. , Stuber Garret D. 
Published: January 2023

AbstractHead-fixed behavioral experiments in rodents permit unparalleled experimental control, precise measurement of behavior, and concurrent modulation and measurement of neural activity. Here we present OHRBETS (Open-Source Head-fixed Rodent Behavioral Experimental Training System; pronounced ‘Orbitz’), a low-cost, open-source ecosystem of hardware and software to flexibly pursue the neural basis of a variety of motivated behaviors. Head-fixed mice tested with OHRBETS displayed operant conditioning for caloric reward that replicates core behavioral phenotypes observed during freely moving conditions. OHRBETS also permits for optogenetic intracranial self-stimulation under positive or negative operant conditioning procedures and real-time place preference behavior, like that observed in freely moving assays. In a multi-spout brief-access consumption task, mice displayed licking as a function of concentration of sucrose, quinine, and sodium chloride, with licking modulated by homeostatic or circadian influences. Finally, to highlight the functionality of OHRBETS, we measured mesolimbic dopamine signals during the multi-spout brief-access task that display strong correlations with relative solution value and magnitude of consumption. All designs, programs, and instructions are provided freely online. This customizable ecosystem enables replicable operant and consummatory behaviors and can be incorporated with methods to perturb and record neural dynamicsin vivo.Impact StatementA customizable open-source hardware and software ecosystem for conducting diverse head-fixed behavioral experiments in mice.
Building modern coexistence theory from the ground up: the role of community assembly
Authors: Spaak Jurg W. , Schreiber Sebastian J. 
Published: January 2023

AbstractModern coexistence theory (MCT) is one of the leading methods to understand species coexistence. It uses invasion growth rates – the average, per-capita growth rate of a rare species – to identify when and why species coexist. Despite significant advances in dissecting coexistence mechanisms when coexistence occurs, MCT relies on a “mutual invasibility” condition designed for two species communities, but poorly defined for species rich communities. Here, we review well-known issues with this component of MCT and propose a solution based on recent mathematical advances. We propose a clear framework for expanding MCT to species rich communities and for understanding invasion resistance as well as coexistence, especially for communities which could not be analyzed with MCT so far. Using two data-driven community models from the literature, we illustrate the utility of our framework and highlight the opportunities for bridging the fields of community assembly and species coexistence.Statement of authorship: Studied conceived jointly by JWS and SJS. JWS and SJS wrote the manuscript together. JWS wrote the python code and SJS wrote R code.Data accessibility: All computer code used in this manuscript will be made publicly available on figshare.Niche and fitness differences | Storage effect | Coexistence
Evidence of Lactate Shuttling in the Human Brain using Hyperpolarized13C-MRI
Authors: Uthayakumar Biranavan , Soliman Hany , Chen Albert P. , Bragagnolo Nadia , Endre Ruby , Perks William J. , Ma Nathan , Heyn Chris , Cunningham Charles H. 
Published: January 2023

AbstractPurposeTo test the hypothesis that lactate shuttling contributes to the13C-lactate and13C-bicarbonate signal observed in the awake human brain using hyperpolarized13C MRI.MethodsHealthy human volunteers (n = 6) were scanned twice using hyperpolarized13C-MRI, with reduced radiofrequency saturation of13C-lactate on one set of scans.13C-lactate,13C-bicarbonate, and13C-pyruvate signals for 132 brain regions across each set of scans were compared using a clustered Wilcoxon sum rank test.ResultsReduced13C-lactate radiofrequency saturation resulted in a significantly greater13C-bicarbonate signal (p= 0.04). These changes were observed across the majority of brain regions.ConclusionRadiofrequency saturation of13C-lactate leads to a decrease in13C-bicarbonate signal, demonstrating that the13C-lactate generated from the injected13C-pyruvate is being converted back to13C-pyruvate and oxidized throughout the human brain.
Anchoring the mean generation time in the SEIR to mitigate biases in ℜ0estimates due to uncertainty in the distribution of the epidemiological delays
Authors: Andrade Jair , Duggan Jim 
Published: January 2023

AbstractThe basic reproduction number,ℜ0, is of paramount importance in the study of infectious disease dynamics. Primarily,ℜ0serves as an indicator of the transmission potential of an emerging infectious disease and the effort required to control the invading pathogen. However, its estimates from compartmental models are strongly conditioned by assumptions in the model structure, such as the distributions of the latent and infectious periods (epidemiological delays). To further complicate matters, models with dissimilar delay structures produce equivalent incidence dynamics. Following a simulation study, we reveal that the nature of such equivalency stems from a linear relationship betweenℜ0and the mean generation time, along with adjustments to other parameters in the model. Leveraging this knowledge, we propose and successfully test an alternative parameterisation of the SEIR model that produces accurateℜ0estimates regardless of the distribution of the epidemiological delays, at the expense of biases in other quantities deemed of lesser importance. We further explore this approach’s robustness by testing various transmissibility levels, generation times, and data fidelity (overdispersion). Finally, we apply the proposed approach to data from the 1918 influenza pandemic. We anticipate that this work will mitigate biases in estimatingℜ0.
Retinal ganglion cells undergo cell type–specific functional changes in a biophysically detailed model of retinal degeneration
Authors: Xu Aiwen , Beyeler Michael 
Published: January 2023

ABSTRACTUnderstanding the retina in health and disease is a key issue for neuroscience and neuroengineering applications such as retinal prostheses. During degeneration, the retinal network undergoes complex and multi-stage neuroanatomical alterations, which drastically impact the retinal ganglion cell (RGC) response and are of clinical importance. Here we present a biophysically detailedin silicomodel of retinal degeneration that simulates the network-level response to both light and electrical stimulation as a function of disease progression. The model is not only able to reproduce common findings about RGC activity in the degenerated retina, such as hyperactivity and increased electrical thresholds, but also offers testable predictions about the underlying neuroanatomical mechanisms. Overall, our findings demonstrate how biophysical changes associated with retinal degeneration affect retinal responses to both light and electrical stimulation, which may further our understanding of visual processing in the retina as well as inform the design and application of retinal prostheses.
Shared patterns of population genomic variation and phenotypic response across rapid range expansions in two invasive lady beetle species
Authors: Jones Angela G. , Obrycki John. J. , Sethuraman Arun , Weisrock David W. 
Published: January 2023

AbstractNon-native lady beetle species have often been introduced, with variable success, into North America for biological control of aphids, scales, whiteflies, and other agricultural pests. Two predatory lady beetle species,Propylea quatuordecimpunctataandHippodamia variegata, both originating from Eurasia, were first discovered near Montreal, Quebec, in North America in 1968 and 1984, respectively, and have since expanded into northeastern North America and the midwestern United States. In this study, we estimate the range-wide population structure, establishment and range-expansion, and recent evolutionary history of these species of non-native lady beetles using reduced representation genotyping-by-sequencing via ddRADseq. In addition, we quantified the responses to a key abiotic factor, photoperiod, that regulates adult reproductive diapause in these two species and may influence their latitudinal distribution and spread in North America. Our analyses detect (1) non-significant genetic differentiation and divergence among North American populations, (2) evidence of reduced contemporary gene flow within the continental US, (3) significant phenotypic differences in diapause induction despite genetic similarities across sampled populations.
Transfer learning in heterogeneous drug-target interaction predictions using federated boosting
Authors: Sándor Dániel , Antal Péter 
Published: January 2023

AbstractIn multitask federated learning, when small amounts of data are available, it can be harder to achieve proper predictive performance, especially if the clients’ tasks are different. However, task heterogeneity is common in modern Drug-Target interaction (DTI) prediction problems. As the data available for DTI tasks are sparse, it can be challenging for clients to synchronize the tasks used for training. In our method, we used boosting to enhance transfer in the multitask scenario and adapted it to a federated environment, allowing clients to train models without having to agree on the output dimensions. Boosting uses adaptive weighting of the data to train an ensemble of predictors. Weighting data boosting can induce the selection of important tasks when shaping a model’s latent representation. This way boosting contributes to the weighting of tasks on a client level and enhances transfer, while traditional federated algorithms can be used on a global level. We evaluate our results extensively on the tyrosine kinase assays of the KIBA data set to get a clear picture of connections between boosting federated learning and transfer learning.
Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis
Authors: Hu Yuzhao , Rosado Daniele , Lindbäck Louise N. , Micko Julie , Pedmale Ullas V. 
Published: January 2023

SUMMARYCryptochromes (CRYs) are evolutionarily conserved blue-light receptors that evolved from bacterial photolyases that repair damaged DNA. Today, CRYs have lost their ability to repair damaged DNA; however, prior reports suggest that human CRYs can respond to DNA damage. Currently, the role of CRYs in the DNA damage response (DDR) is lacking, especially in plants. Therefore, we evaluated the role of plant CRYs in DDR along with UBP12/13 deubiquitinases, which interact with and regulate the CRY2 protein. We found thatcry1cry2was hypersensitive, whileubp12ubp13was hyposensitive to UVC-induced DNA damage. Elevated UV-induced cyclobutane pyrimidine dimers (CPDs) and the lack of DNA repair protein RAD51 accumulation incry1cry2plants indicate that CRYs are required for DNA repair. On the contrary, CPD levels diminished and RAD51 protein levels elevated in plants lacking UBP12 and UBP13, indicating their role in DDR repression. Temporal transcriptomic analysis revealed that DDR-induced transcriptional responses were subdued incry1cry2, but elevated inubp12ubp13compared to WT. Through transcriptional modeling of the timecourse transcriptome, we found that genes quickly induced by UVC (15 min) are targets of CAMTA 1-3 transcription factors, which we found are required for DDR. This transcriptional regulation seems, however, diminished in thecry1cry2mutant, indicating that CAMTAs are required for CRY2-mediated DDR. Furthermore, we observed enhanced CRY2-UBP13 interaction and formation of CRY2 nuclear speckles under UVC, suggesting that UVC activates CRY2 similarly to blue light. Together, our data reveal the temporal dynamics of the transcriptional events underlying UVC-induced genotoxicity and expand our knowledge of the role of CRY and UBP12/13 in DDR.
Impaired polyamine metabolism causes behavioral and neuroanatomical defects in a novel mouse model of Snyder-Robinson Syndrome
Authors: Akinyele Oluwaseun , Munir Anushe , Johnson Marie A. , Perez Megan S. , Gao Yuan , Foley Jackson R. , Wu Yijen , Murray-Stewart Tracy , Casero Robert A. , Bayir Hulya , Kemaladewi Dwi U. 
Published: January 2023

AbstractPolyamines (putrescine, spermidine, and spermine) are essential molecules for normal cellular functions and are subject to strict metabolic regulation. Mutations in the gene encoding spermine synthase (SMS) lead to accumulation of spermidine in an X-linked recessive disorder known as Snyder-Robinson syndrome (SRS). Presently, no treatments exist for this rare disease that manifests with a spectrum of symptoms including intellectual disability, developmental delay, thin habitus, and low muscle tone. The development of therapeutic interventions for SRS will require a suitable disease-specific animal model that recapitulates many of the abnormalities observed in patients.Here, we characterize the molecular, behavioral, and neuroanatomical features of a mouse model with a missense mutation inSmsgene that results in a glycine-to-serine substitution at position 56 (G56S) of the SMS protein. Mice harboring this mutation exhibit a complete loss of SMS protein and elevated spermidine/spermine ratio in skeletal muscles and the brain. In addition, the G56S mice demonstrate increased anxiety, impaired learning, and decreased explorative behavior in fear conditioning, Morris water maze, and open field tests, respectively. Furthermore, these mice failed to gain weight over time and exhibit abnormalities in brain structure and bone density. Transcriptomic analysis of the cerebral cortex revealed downregulation of genes associated with mitochondrial oxidative phosphorylation and ribosomal protein synthesis. Our findings also revealed impaired mitochondrial bioenergetics in fibroblasts isolated from the G56S mice, indicating a correlation between these processes in the affected mice. Collectively, our findings establish the first in-depth characterization of an SRS preclinical mouse model that identifies cellular processes that could be targeted for future therapeutic development.