bluuebunny/crossref_metadata_2025_split huggingface dataset:
The BioGenome Portal: a web-based platform for biodiversity genomics data management
Authors: Righi Emilio , Guigó Roderic 
Published: December 2023

ABSTRACTBiodiversity genomics projects are underway with the aim of sequencing the genomes of all eukaryotic species on Earth. Here we describe the BioGenome Portal, a web-based application to facilitate organization and access to the data produced by biodiversity genomics projects. The portal integrates user-generated data with data deposited in public repositories. The portal generates sequence status reports that can be eventually ingested by designated meta-data tracking systems, facilitating the coordination task of these systems. The portal is open-source and fully customizable. It can be deployed at any site with minimum effort, contributing to the democratization of biodiversity genomics projects. Here, we illustrate the features of the BioGenome Portal through two specific instances. One instance corresponds to the Earth Biogenome Project, the worldwide umbrella for most biodiversity genomics projects. The other instance corresponds to the Catalan Initiative for the Earth Biogenome Project, a regional project aiming to sequencing the genomes of the species of the Catalan Linguistic Area.
An AAV capsid reprogrammed to bind human Transferrin Receptor mediates brain-wide gene delivery
Authors: Huang Qin , Chan Ken Y. , Lou Shan , Keyes Casey , Wu Jason , Botticello-Romero Nuria R , Zheng Qingxia , Johnston Jencilin , Mills Allan , Brauer Pamela P. , Clouse Gabrielle , Pacouret Simon , Harvey John W. , Beddow Thomas , Hurley Jenna K. , Tobey Isabelle G. , Powell Megan , Chen Albert T. , Barry Andrew J. , Eid Fatma-Elzahraa , Chan Yujia A. , Deverman Benjamin E. 
Published: December 2023

AbstractDeveloping vehicles that efficiently deliver genes throughout the human central nervous system (CNS) will broaden the range of treatable genetic diseases. We engineered an AAV capsid, BI-hTFR1, that binds human Transferrin Receptor (TfR1), a protein expressed on the blood-brain barrier (BBB). BI-hTFR1 was actively transported across a human brain endothelial cell layer and, relative to AAV9, provided 40–50 times greater reporter expression in the CNS of humanTFRCknock-in mice. The enhanced tropism was CNS-specific and absent in wild type mice. When used to deliverGBA1, mutations of which cause Gaucher disease and are linked to Parkinson’s disease, BI-hTFR1 substantially increased brain and cerebrospinal fluid glucocerebrosidase activity compared to AAV9. These findings establish BI-hTFR1 as a promising vector for human CNS gene therapy.
Spatially Dependent Tissue Distribution of Thyroid Hormones by Plasma Thyroid Hormone Binding Proteins
Authors: Bagga Anish D. , Johnson Brian P. , Zhang Qiang 
Published: December 2023

AbstractPlasma thyroid hormone (TH) binding proteins (THBPs), including thyroxine-binding globulin (TBG), transthyretin (TTR), and albumin (ALB), carry THs to extrathyroidal sites, where THs are unloaded locally and then taken up via membrane transporters into the tissue proper. The respective roles of THBPs in supplying THs for tissue uptake are not completely understood. To investigate this, we developed a spatial human physiologically based kinetic (PBK) model of THs, which produces several novel findings.(1)Contrary to postulations that TTR and/or ALB are the major local T4 contributors, the three THBPs may unload comparable amounts of T4 inLiver, a rapidly perfused organ; however, their contributions in slowly perfused tissues follow the order of abundances of T4TBG, T4TTR, and T4ALB. The T3 amounts unloaded from or loaded onto THBPs in a tissue acting as a T3 sink or source respectively follow the order of abundance of T3TBG, T3ALB, and T3TTR regardless of perfusion rate.(2)Any THBP alone is sufficient to maintain spatially uniform TH tissue distributions.(3)The TH amounts unloaded by each THBP species are spatially dependent and nonlinear in a tissue, with ALB being the dominant contributor near the arterial end but conceding to TBG near the venous end.(4)Spatial gradients of TH transporters and metabolic enzymes may modulate these contributions, producing spatially invariant or heterogeneous TH tissue concentrations depending on whether the blood-tissue TH exchange operates in near-equilibrium mode. In summary, our modeling provides novel insights into the differential roles of THBPs in local TH tissue distribution.Key PointsThyroxine-binding globulin (TBG), transthyretin (TTR), and albumin (ALB) are plasma thyroid hormone (TH) binding proteins (THBPs) that carry THs from the thyroid gland to extrathyroidal tissues.The respective roles of the 3 THBP species in unloading THs once arriving at a tissue are not completely understood.Here we developed a spatial human kinetic model of THs and showed that the three THBPs may unload comparable amounts of thyroxine (T4) in the liver but TBG is dominant in contributing T4 in tissues slowly perfused by blood as well as in contributing triiodothyronine (T3) regardless of the tissue’s perfusion rate.The TH amounts unloaded by each THBP species are spatially dependent and nonlinear, with ALB being the dominant contributor near the arterial end but conceding to TBG near the venous end in a tissue.Our model provides novel insights into the differential roles of THBPs in local TH tissue distribution.
Variation in echolocation call emission of Neotropical insect-eating bats in response to shifting ambient temperatures
Authors: Iturralde Pólit Paula , Araya-Salas Marcelo , Goerlitz Holger R. , Chaverri Gloriana 
Published: December 2023

ABSTRACTThe sensory systems of animals are essential for them to respond to environmental cues and signals. However, their functionality might be altered by climate change. Most bats, for example, rely on acoustic signal emission for acquiring food, but their high-frequency echolocation calls are strongly attenuated in the air. Attenuation in air changes with changing weather conditions, which can lead to shifts in echo-based prey detection distance. However, bats adjust call parameters to the task and environment, and this behavioural plasticity may also help them to counteract potential increases in sound attenuation to keep echo detectability constant. We explored this ability in a community of insectivorous bats in a montane forest of Costa Rica. We recorded bat echolocation calls in response to experimentally increased temperatures, simulating intermediate and arguably realistic projected climate change scenarios. We calculated atmospheric attenuation and detection distance for each temperature and echolocation call. We found some changes in source level and call duration, yet not in peak frequency, and responses were not consistent across species with increasing atmospheric attenuation. This might be explained by several non-mutually exclusive reasons, including that the experimental increase in temperature and change of atmospheric attenuation were not sufficient to affect close-range prey detection. Ultimately, this study contributes to our understanding of sensory system adaptation under the pressure imposed by climate change.SUMMARY STATEMENTStudying adjustments in bats’ call parameters can reveal responses to the pressure imposed by climate change.
Order of arrival and nutrient supply alter outcomes of coinfection with two fungal pathogens
Authors: Green Elizabeth T. , Grunberg Rita L. , Mitchell Charles E. 
Published: December 2023

AbstractA pathogen arriving on a host typically encounters a diverse community of microbes that can shape priority effects, other within-host interactions, and infection outcomes. In plants, environmental nutrients can drive tradeoffs between host growth and defense and can mediate interactions between coinfecting pathogens. Nutrients may thus alter the outcome of pathogen priority effects for the host, but this possibility has received little experimental investigation. To disentangle the relationship between nutrient availability and coinfection dynamics, we factorially manipulated nutrient availability and order of arrival of two foliar fungal pathogens (Rhizoctonia solaniandColletotrichum cereale) on the host grass tall fescue (Festuca arundinacea) and tracked disease outcomes. Overall,C. cerealeinfection facilitated infection byR. solani, increasing its infection rate regardless of their order of inoculation. Additionally, simultaneous andC. cereale-first inoculations decreased plant growth and – in plants that did not receive nutrient addition – increased leaf nitrogen concentrations compared to uninoculated plants. Nutrient addition did not influence infection rates, severity of infection, or plant biomass. These findings highlight the importance of understanding the intricate associations between the order of pathogen arrival, host nutrient availability, and host defense to better predict infection outcomes.
How to control unpredictable others in court-net sports
Authors: Yamamoto Yuji , Yokoyama Keiko , Kijima Akifumi , Okumura Motoki , Shima Hiroyuki , Gohara Kazutoshi 
Published: December 2023

AbstractCompetition in sports does not involve a single solution because individuals aim to behave unpredictably, thereby preventing others from predicting their actions. This study determined how individuals in court net sports tried to control others’ unpredictable behavior, thereby addressing the gap of the lack of clarity about strategies employed by individuals in competitive situations. We employed a switching hybrid dynamics model, considering external inputs when analyzing individual behaviors. The study shows that skilled individuals, unlike intermediate players, exhibit greater regularity in their behavior, lead others to anticipate this regularity, and employ strategies to disrupt these expectations. This strategy exploits the principles of active human inference, implying that competition involves cooperation. We revealed this by analyzing both human decision-making and behavior in actual matches as discrete and continuous dynamical systems. This strategy helps policymakers adopt a new policy targeting cooperation with competitors, which would increase competitiveness in our daily lives.
The Impact of Race, Ethnicity, and Socioeconomic Status on the Severity of Menopause Symptoms: A Study of 68,864 Women
Authors: Kochersberger Alison , Coakley Aeowynn , Millheiser Leah , Morris Jerrine R. , Manneh Claire , Jackson Alicia , Garrison Jennifer L. , Hariton Eduardo 
Published: December 2023

AbstractObjectiveTo evaluate how race, ethnicity, and socioeconomic status (SES) affect the severity of menopause symptoms in a large, diverse sample of women.MethodsFor this cross-sectional study conducted between March 24, 2019, and January 13, 2023, a total of 68,864 women were enrolled from the Evernow online telehealth platform. Participants underwent a clinical intake survey, which encompassed demographic information, detailed medical questionnaires, and a modified Menopause Rating Scale (MRS). The modified scale was adapted for ease of use online and is available in the supplementary material along with the full intake. Symptom severity was evaluated using a multivariate binomial generalized linear model, accounting for factors such as race, ethnicity, age, BMI, smoking status, bilateral oophorectomy status, and SES. Odds ratios and confidence intervals were calculated based on the linear regression coefficients.ResultsOf the participants, 67,867 (98.6%) were included in the analysis after excluding outliers and those with unknown oophorectomy status. The majority of respondents identified as White (77.4%), followed by Hispanic (9.0%), Black (6.7%), two or more races/ethnicities (4.4%), Asian (1.2%), Indigenous/First Nations (0.8%), Middle Eastern (0.3%), and South Asian (0.2%). Notably, individuals identifying as Black, Hispanic, Indigenous/First Nations, Middle Eastern, or with two or more races/ethnicities reported higher levels of symptom severity compared to their White counterparts. Conversely, Asian and South Asian participants reported lower symptom severity. Even after incorporating SES into the linear model, racial and ethnic groups with lower SES (Black, Hispanic, Indigenous, and multiple ethnicities) exhibited slight shifts in odds ratios, while maintaining high statistical significance.ConclusionsOur study suggests that the relationship between race and ethnicity and the severity of menopause symptoms is not solely explained by differences in SES but is itself an independent factor. Understanding and addressing social, cultural, and economic factors is crucial to reduce disparities in menopausal symptoms.
Identification of new proviral and antiviral factors through the study of the Dicer-2 interactomein vivoduring viral infection inDrosophila melanogaster
Authors: Rousseau Claire , Lauret Émilie , Kuhn Lauriane , Chicher Johana , Hammann Philippe , Meignin Carine 
Published: December 2023

ABSTRACTRNA interference, which has a major role in the control of viral infection in insects, is initialized by the sensing of double stranded RNA (dsRNA) by the RNAse III enzyme Dicer-2. Although manyin vitrostudies have helped understand how Dicer-2 is able to discriminate between different dsRNA substrate termini, much less is known about how this translates to thein vivorecognition of viral dsRNA. Indeed, although Dicer-2 associates with several dsRNA-binding proteins (dsRBPs) that can modify its specificity for a substrate, it remains unknown how Dicer-2 is able to recognize the protected termini of viral dsRNAs. In order to study how the ribonucleoprotein network of Dicer-2 impacts antiviral immunity, we used an IP-MS approach to identifyin vivointeractants of different versions of GFP::Dicer-2 in transgenic lines. We provide a global overview of the partners of Dicer-2in vivo, and reveal how this interactome is modulated by different factors such as the viral infection and/or different point mutations inactivating the helicase or RNase III domains of GFP::Dicer-2. Our analysis uncovers several previously unknown Dicer-2 interactants associated with RNA granules (i.e. Me31B, Rump, eIF4E1 & Syp). Functional characterization of the candidates reveals pro- and antiviral factors in the context of the infection by the picorna-like DCV virus. In particular, the protein Rasputin has been identified as a novel antiviral candidate. The resources provided by this work can be used to gain a better understanding of the molecular complexes assembled around Dicer-2 in the context of antiviral RNAi and beyond.
Switching perspective: Comparing ground-level and bird’s-eye views for bumblebees navigating dense environments
Authors: Sonntag Annkathrin , Sauzet Odile , Lihoreau Mathieu , Egelhaaf Martin , Bertrand Olivier 
Published: December 2023

AbstractAnimals navigating in three dimensions encounter different perspectives of their world, often transitioning from bird’s eye views at higher altitudes to ground views closer to the ground. How they integrate this information to pinpoint a goal location is virtually unknown. Here we tested the ability of bumblebees to use both types of views when homing in a dense environment in the vicinity of their inconspicuous nest entrance. Our combined modelling and experimental approach examined various views for localising a goal in dense settings. Whereas, bird’s-eye views performed best in simulations of current nest-centered snapshot homing models, behavioural experiments revealed that bumblebees predominantly relied on ground views when pinpointing nest entrances in dense environments. These findings reveal the limitations of snapshot-homing models and suggest that bumblebees use a combination of navigational tools to successfully find their way home in dense environments. This is not only relevant for understanding bee navigation, but also for other animals and humans navigating in 3D as well as the development of technologies inspired by natural systems, such as autonomous flying robots.
Phase diagrams of bone remodeling using a 3D stochastic cellular automaton
Authors: Heller Anna-Dorothea , Valleriani Angelo , Cipitria Amaia 
Published: December 2023

AbstractWe propose a 3D stochastic cellular automaton model, governed by evolutionary game theory, to simulate bone remodeling dynamics. The model includes four voxel states:Formation, Quiescence, Resorption, andEnvironment. We simulate theResorptionandFormationprocesses on separate time scales to explore the parameter space and derive a phase diagram that illustrates the sensitivity of these processes to parameter changes. Combining these results, we simulate a full bone remodeling cycle. Furthermore, we show the importance of modeling small neighborhoods for studying local bone microenvironment controls. This model can guide experimental design and, in combination with other models, it could assist to further explore external impacts on bone remodeling. Consequently, this model contributes to an improved understanding of complex dynamics in bone remodeling dynamics and exploring alterations due to disease or drug treatment.Author summaryFunctional well-balanced bone remodeling is crucial for a healthy skeleton. Understanding the various causes for the disruption of this complex process requires models that combine behavior on micro- and macro-level. We propose a 3D stochastic cellular automaton model, where each voxel can take one of four different states representing phases of bone remodeling:Formation, Quiescence, ResorptionandEnvironment. With a qualitative analysis, we show how and when small changes in key interaction parameters can make the difference between healthy and pathological bone remodeling. We also highlight the importance of spatial modeling and the size of the neighborhood for investigating local mechanisms. Our proposed model opens the window to explore the complex interplay of factors essential for healthy bone remodeling and potential alterations due to disease or drug treatment. In the long term this could help with the development of new treatment options for bone diseases.
Western diet feeding since adolescence impairs functional hyperemia probed by functional ultrasound imaging at adulthood and middle age: rescue by a balanced ω-3:ω-6 polyunsaturated fatty acids ratio in the diet
Authors: Soleimanzad Haleh , Morisset Clémentine , Montaner Mireia , Pain Frédéric , Magnan Christophe , Tanter Mickaël , Gurden Hirac 
Published: December 2023

AbstractObesity is a devastating worldwide metabolic disease, with the highest prevalence in children and adolescence. Obesity impacts neuronal function but the fate of functional hyperemia, a vital mechanism making possible cerebral blood supply to active brain areas, is unknown in organisms fed a high caloric Western Diet (WD) since adolescence. We mapped changes in cerebral blood volume (CBV) in the somatosensory cortex in response to whiskers stimulation in adolescent, adult and middle-aged mice fed a WD since adolescence. To this aim, we used non-invasive and high-resolution functional ultrasound imaging (fUS). Functional hyperemia is compromised as early as 3 weeks of WD and remains impaired thereafter. Starting WD in adult mice does not trigger the profound impairment in sensory-evoked CBV observed in young mice, suggesting a cerebrovascular vulnerability to WD during adolescence. A balanced ω-6:ω-3 polyunsaturated fatty acids ratio in WD achieved by docosahexaenoic acid supplementation is efficient to restore glucose homeostasis and functional hyperemia in adults.
TheZea maysPeptideAtlas – a new maize community resource
Authors: van Wijk Klaas J. , Leppert Tami , Sun Zhi , Guzchenko Isabell , Debley Erica , Sauermann Georgia , Routray Pratyush , Mendoza Luis , Sun Qi , Deutsch Eric W. 
Published: December 2023

ABSTRACTWe developed the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize were collected from ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds, including the inbred lines B73 and W22, many hybrids and their respective parents. Samples were collected from field trials, controlled environmental conditions, a range of (a)biotic conditions and different tissues, cell types and subcellular fractions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of the proteins (one isoform per protein coding gene) in the most recent B73 nuclear genome annotation (v5). Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other searched B73 genome annotations will aid to improve maize genome annotation. We also illustrate high confidence detection of unique W22 proteins. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, K-hydroxyisobutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical and biological metadata. This new PeptideAtlas is integrated with community resources including MaizeGDB athttps://www.maizegdb.org/and a peptide track in JBrowse.