bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the global prevalence of wild birds in trade
Authors: Donald Paul F. , Fernando Eresha , Brown Lauren , Busana Michela , Butchart Stuart H.M. , Chng Serene , de la Colina Alicia , Ferreira Juliana Machado , Jain Anuj , Jones Victoria R. , Lapido Rocio , Malsch Kelly , McDougall Amy , Muccio Colum , Nguyen Dao , Outhwaite Willow , Petrovan Silviu O. , Stafford Ciara , Sutherland William J. , Tallowin Oliver , Safford Roger 
Published: August 2023

AbstractTrade represents a significant threat to many wild species and is often clandestine and poorly monitored. Information on which species are most prevalent in trade, and potentially threatened by it, therefore remains fragmentary. We mobilised seven global datasets on birds in trade to identify the species or groups of species that might be at particular risk. These datasets sample different parts of the broad trade spectrum but we nevertheless find a statistically strong congruence between them in which species are recorded in trade. Furthermore, the frequency with which species are recorded within datasets is positively correlated with their occurrence across datasets. This allows us to propose a trade prevalence score that can be applied to all bird species globally. This score discriminates well between species known from semi-independent assessments to be heavily or unsustainably traded and all other species. Globally, 45.1% of all bird species, and 36.7% of globally threatened bird species, were recorded in at least one of the seven datasets. Species listed in Appendices I or II of CITES, species with large geographical distributions and non-songbirds had higher trade prevalence scores. Speciose orders with high mean trade prevalence scores include the Falconiformes, Psittaciformes, Accipitriformes, Anseriformes, Bucerotiformes and Strigiformes. Despite their low mean prevalence score, Passeriformes accounted for the highest overall number of traded species of any order but had low representation in CITES Appendices. Geographical hotspots where large numbers of traded species co-occur differed between songbirds (South-East Asia and Eurasia) and non-songbirds (central South America, sub-Saharan Africa and India). This first attempt to quantify and map the relative prevalence in trade of all bird species globally can be used to identify species and groups of species which may be at particular risk of harm from trade and can inform conservation and policy interventions to reduce its adverse impacts.Article impact statementThe first metric to estimate the prevalence in trade of all the world’s bird species is presented.
Innate sleep apnoea in spontaneously hypertensive rats is associated with microvascular rarefaction and neuronal loss in the preBötzinger Complex
Authors: Roberts Reno , Huckstepp Robert T. R. 
Published: August 2023

AbstractSleep apnoea is a major threat to physical health and carries a significant economic burden. These impacts are worsened by its interaction with, and induction of, its comorbidities. Sleep apnoea holds a bidirectional relationship with hypertension which drives atherosclerosis, ultimately culminating in vascular dementia. To enable a better understanding of this sequalae of events, we investigated innate sleep apnoea in spontaneously hypertensive rats (SHRs), which have a range of cardiovascular disorders. SHRs displayed a higher degree of sleep disordered breathing, which emanates from poor vascular health leading to a loss of preBötC neurons. This model also displays small vessel white matter disease, a form of vascular dementia, likely associated with neuroinflammation in the hippocampus and the related deficits in both long- and short-term memory. Therefore, hypertension induces sleep apnoea through vascular damage in the respiratory column, culminating in neuronal loss in the inspiratory oscillator. This induction of sleep apnoea which in turn will independently exacerbate hypertension and neural inflammation, increasing the rate of vascular dementia.
Mapping of Facial and Vocal Processing in Common Marmosets with ultra-high field fMRI
Authors: Dureux Audrey , Zanini Alessandro , Everling Stefan 
Published: August 2023

SummaryPrimate communication relies on multimodal cues, such as vision and audition, to facilitate the exchange of intentions, enable social interactions, avoid predators, and foster group cohesion during daily activities. Understanding the integration of facial and vocal signals is pivotal to comprehend social interaction. In this study, we acquired whole-brain ultra-high field (9.4T) fMRI data from awake marmosets (Callithrix jacchus) to explore brain responses to unimodal and combined facial and vocal stimuli. Our findings reveal that the multisensory condition not only intensified activations in the occipito-temporal ‘face patches’ and auditory ‘voice patches’ but also engaged a more extensive network that included additional parietal, prefrontal and cingulate areas, compared to the summed responses of the unimodal conditions. By uncovering the neural network underlying multisensory audiovisual integration in marmosets, this study highlights the efficiency and adaptability of the marmoset brain in processing facial and vocal social signals, providing significant insights into primate social communication.
Evolutionary formation of a humande novoopen reading frame from a non-primate non-coding genomic region that proceeds via biased random mutations
Authors: Delihas Nicholas 
Published: August 2023

AbstractTwo open reading frames (ORFs) of evolutionary interest stem from the human geneSMIM45. An investigation shows that one consists of an ultra-conserved 68 amino acid (aa) sequence that dates back to the amphibians, ∼192 MYA. In contrast, the other, an ORF of 107 aa develops slowly during primate evolution. An early developmental stage of the 107 aa ORF has been detected in non-primate genomes. In the mouse, it consists of a small sequence homologous to a segment of the human 107 aa ORF, the aa sequence SGLE*VTVYGGGVQKGKT. This suggests the evolutionary root of the 107 aa ORF dates to an ancestor of the mouse; root species have been proposed based on the presence or absence of the early developmental sequence in ancestors. The formation of the complete 107 aa ORF during primate evolution is also outlined. Found is growth of the 107 aa ORF by biased random mutations. The delineation of mutations occurring during development of the 107 aa ORF can provide a model for the evolutionary formation of ORFs ofde novoprotein genes.
Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA
Authors: Camara Momodou B. , Lange Bret , Yesselman Joseph D. , Eichhorn Catherine D. 
Published: August 2023

AbstractStructural plasticity is integral to RNA function; however, there are currently few methods to quantitatively resolve RNAs that have multiple structural states. NMR spectroscopy is a powerful approach for resolving conformational ensembles but is size-limited. Chemical probing is well-suited for large RNAs but provides limited structural and no kinetics information. Here, we integrate the two approaches to visualize a two-state conformational ensemble for the central stem-loop 3 (SL3) of 7SK RNA, a critical element for 7SK RNA function in transcription regulation. We find that the SL3 distal end exchanges between two equally populated yet structurally distinct states in both isolated SL3 constructs and full-length 7SK RNA. We rationally designed constructs that lock SL3 into a single state and demonstrate that both chemical probing and NMR data fit to a linear combination of the two states. Comparison of vertebrate 7SK RNA sequences shows conservation of both states, suggesting functional importance. These results provide new insights into 7SK RNA structural dynamics and demonstrate the utility of integrating chemical probing with NMR spectroscopy to gain quantitative insights into RNA conformational ensembles.
Local interneurons in the murine visual thalamus have diverse receptive fields and can provide feature selective inhibition to relay cells
Authors: Gorin Alexis S. , Miao Yizhan , Ahn Seohee , Suresh Vandana , Su Yinan , Ciftcioglu Ulas M. , Sommer Friedrich T. , Hirsch Judith A. 
Published: August 2023

SummaryBy influencing the type and quality of information that relay cells transmit, local interneurons in thalamus have a powerful impact on cortex. To define the sensory features that these inhibitory neurons encode, we mapped receptive fields of optogenetically identified cells in the murine dorsolateral geniculate nucleus. Although few in number, local interneurons had diverse types of receptive fields, like their counterpart relay cells. This result differs markedly from visual cortex, where inhibitory cells are typically less selective than excitatory cells. To explore how thalamic interneurons might converge on relay cells, we took a computational approach. Using an evolutionary algorithm to search through a library of interneuron models generated from our results, we show that aggregated output from different groups of local interneurons can simulate the inhibitory component of the relay cell’s receptive field. Thus, our work provides proof-of-concept that groups of diverse interneurons can supply feature-specific inhibition to relay cells.
A leaky gut dysregulates gene networks in the brain associated with immune activation, oxidative stress, and myelination in a mouse model of colitis
Authors: Boles Jake Sondag , Krueger Maeve E. , Jernigan Janna E. , Cole Cassandra L. , Neighbarger Noelle K. , Huarte Oihane Uriarte , Tansey Malú Gámez 
Published: August 2023

AbstractThe gut and brain are increasingly linked in human disease, with neuropsychiatric conditions classically attributed to the brain showing an involvement of the intestine and inflammatory bowel diseases (IBDs) displaying an ever-expanding list of neurological comorbidities. To identify molecular systems that underpin this gut-brain connection and thus discover therapeutic targets, experimental models of gut dysfunction must be evaluated for brain effects. In the present study, we examine disturbances along the gut-brain axis in a widely used murine model of colitis, the dextran sodium sulfate (DSS) model, using high-throughput transcriptomics and an unbiased network analysis strategy coupled with standard biochemical outcome measures to achieve a comprehensive approach to identify key disease processes in both colon and brain. We examine the reproducibility of colitis induction with this model and its resulting genetic programs during different phases of disease, finding that DSS-induced colitis is largely reproducible with a few site-specific molecular features. We focus on the circulating immune system as the intermediary between the gut and brain, which exhibits an activation of pro-inflammatory innate immunity during colitis. Our unbiased transcriptomics analysis provides supporting evidence for immune activation in the brain during colitis, suggests that myelination may be a process vulnerable to increased intestinal permeability, and identifies a possible role for oxidative stress and brain oxygenation. Overall, we provide a comprehensive evaluation of multiple systems in a prevalent experimental model of intestinal permeability, which will inform future studies using this model and others, assist in the identification of druggable targets in the gut-brain axis, and contribute to our understanding of the concomitance of intestinal and neuropsychiatric dysfunction.
Effect of Aqueous Garlic Extract on Hyperlipidaemia in Rats: A Randomised Case-Control Study
Authors: Sankarl Gamel , Akyeampong Enoch , Sarhene Micheal , Anai Rexford Kporvie 
Published: August 2023

ABSTRACTThis study aimed to determine the effect of garlic extract on hyperlipidemia in rats. This was a randomised case-control study in 42 rats comprising seven groups with six animals per group. Group I consisted of rats fed with 100% Normal rat chow serving as control, Group II: Butter diet, Group III: Butter diet + Atorvastatin, Group IV: Butter diet + Garlic extract, Group V: rats injected with dexamethasone, Group VI: Dexamethasone + Atorvastatin, Group VII: Dexamethasone + Garlic extract. Blood was collected from all the animals and the separated serum was subjected to the estimations of lipoproteins levels and coronary risk. There was a significant increase in the concentration of TC in the butter control group (BCG) compared to the concentration of the LDL-C (p=0.028) of the normal control group (NCG). The concentration of TG was significantly higher in DCG when compared with TG concentration in NCG (p<0.0001) and BCG (p=0.0002). Total Cholesterol level was significantly higher in BCG when compared to BGG (p<0.0001), BAG (p=0.0001) and NCG (p=0.023) which typifies hypercholesterolemia. Hyperlipidemia was induced by the long-term high-fat diet but lipid levels were reduced after the administration of aqueous garlic extract and atorvastatin.
The aryl hydrocarbon receptor in β-cells mediates the effects of TCDD on glucose homeostasis in mice
Authors: Hoyeck Myriam P , Ching Ma. Enrica Angela , Basu Lahari , Van Allen Kyle , Palaniyandi Jana , Perera Ineli , Poleo-Giorgani Emilia , Hanson Antonio A , Bruin Jennifer E 
Published: August 2023

AbstractChronic exposure to persistent organic pollutants (POPs) is associated with increased incidence of type 2 diabetes, hyperglycemia, and poor insulin secretion in humans. Dioxins and dioxin-like compounds are a broad class of POPs that exert cellular toxicity through activation of the aryl hydrocarbon receptor (AhR). We previously showed that a single high-dose injection of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, aka dioxin; 20 µg/kg)in vivoreduced fasting and glucose-stimulated plasma insulin levels for up to 6 weeks in male and female mice. TCDD-exposed male mice were also modestly hypoglycemic and had increased insulin sensitivity, whereas TCDD-exposed females were transiently glucose intolerant; whether these effects are driven by AhR activation in β-cells requires investigation. Here we exposed female and male β-cell specific AhR knockout (βAhrKO) mice and littermate Ins1-Cre genotype controls (βAhrWT) to a single high dose of 20 µg/kg TCDD and tracked the mice for 6 weeks. We found that deleting AhR from β-cells increased insulin secretionex vivoin female mouse islets and promoted modest weight gain in male mice under baseline conditions. Importantly, high-dose TCDD exposure impaired glucose homeostasis and β-cell function in βAhrWTmice, but these phenotypes were largely abolished in TCDD-exposed βAhrKOmice. Our study demonstrates that AhR signaling in β-cell is important for regulating baseline β-cell function in female mice and energy homeostasis in male mice. We also show that β-cell AhR signaling largely mediates the effects of TCDD on glucose homeostasis in both female and male mice, suggesting that the effects of TCDD on β-cell function/health are driving metabolic phenotypes in peripheral tissues.
Assessing Inter-Individual Genetic Variability in Peach Sugar Metabolism through Reliable Parameter Estimation of a Kinetic Model
Authors: Kanso Hussein , Memah Mohamed-Mahmoud , Baldazzi Valentina , Quilot-Turion Bénédicte , Baey Charlotte 
Published: August 2023

AbstractIntegrating genetic information into dynamical models is key to understand variations among genotypes and improve crop performances face to current agronomic and ecological constraints. A first and necessary step in building gene-to-phenotype models is the calibration of a large number of genotypes. We compared here two different strategies for the calibration of an Ordinary Differential Equations (ODE) kinetic model simulating the accumulation of different sugars during peach fruit development. First, the model was calibrated for each genotype independently using a Genotype-Based (GB) strategy. Two formulations of the problem have been tested, either as a Single-Objective Optimization (GBS) problem or as a Multi-Objective Optimization (GBM) problem. Second, the model was calibrated for all genotypes simultaneously using a Population-Based (PB) strategy. The two strategies were first applied to a set of simulated data and then to a real dataset derived from an interspecific population of 106 peach genotypes. Results showed that the GB strategy allowed for a high goodness of fit for most genotypes, especially in the GBS formulation. However, the estimated parameters suffered from a lack of practical identifiability as independent repetitions of the estimation algorithm did not always converge to the same value for most genotypes. The PB calibration strategy overcame this issue showing a good identifiability of the population parameter values, a goodness of fit comparable to the one obtained with the GB strategy and a good characterisation of parameter variations within the progeny, which is a key to assess the inter-individual genetic variability. These results are an important step towards the development of reliable gene-to-phenotype models.
VelosGT: Edge-Computing for Human Variant Analysis
Authors: Flygare Josh , Born Alex 
Published: August 2023

AbstractVelosGTis a MacOS application to analyze human genomes for genetic mutation and rare disease. It consumes raw read files (fasta/fastq) and returns annotated, functionally prioritized variants in a single step, while significantly out-performing standard pipelines. VelosGTingests short-read data in all common formats (fastq, fasta, fastq.gz, and fasta.gz) as well as paired data. It can perform analyses on single genomes (proband) or trios. The underlying algorithms have been optimized to the extent that it can run directly on a personal computer, with no additional hardware required. This increases convenience and speed because no large uploads or downloads are required. All discovered variants are immediately displayed and searchable within the app. On an average*Mac laptop, VelosGTwill return the results of a high-coverage 30GB read file in under an hour, and a 5GB read file in ten minutes or less. Trios can be computed using the completed child-parent analyses in a few minutes.
Predicting species distributions in the open ocean with convolutional neural networks
Authors: Morand Gaétan , Joly Alexis , Rouyer Tristan , Lorieul Titouan , Barde Julien 
Published: August 2023

AbstractAs biodiversity plummets due to anthropogenic disturbances, the conservation of oceanic species is made harder by limited knowledge of their distributions and migrations. Indeed, tracking species distributions in the open ocean is particularly challenging due to the scarcity of observations and the complex and variable nature of the ocean system. In this study, we propose a new method that leverages deep learning, specifically convolutional neural networks (CNNs), to capture spatial features of environmental variables. This novelty eliminates the need to predefine these features before modelling and creates opportunities to discover unexpected correlations. Our aim is to present the results of the first trial of this method in the open ocean, discuss limitations and provide feedback for future improvements or adjustments.In this case study, we considered 38 taxa comprising pelagic fishes, elasmobranchs, marine mammals, marine turtles and birds. We trained a model to predict probabilities from the environmental conditions at any specific point in space and time, using species occurrence data from the Global Biodiversity Information Facility (GBIF) and environmental data from various sources. These variables included sea surface temperature, chlorophyll concentration, salinity and fifteen others.During the testing phase, the model was applied to environmental data at locations where species occurrences were recorded. The classifier accurately predicted the observed taxon as the most likely taxon in 69% of cases and included the observed taxon among the top three most likely predictions in 89% of cases. These findings show the adequacy of deep learning for species distribution modelling in the open ocean.Additionally, this purely correlative model was then analysed with explicability tools to understand which variables had an influence on the model’s predictions. While variable importance was species-dependent, we identified finite-size Lyapunov exponents (FSLEs), sea surface temperature, pH and salinity as the most influential variables, in that order. These insights can prove valuable for future species-specific ecology studies.
Narrow, but not broad, spectrum resistance and disease reshape phyllosphere bacterial communities
Authors: Bigott Adam F. , Hutton Samuel F. , Vallad Gary , Lankau Rick , Barak Jeri 
Published: August 2023

AbstractThe phyllosphere is a restrictive environment for microbes, resulting in microbial communities typically dominated by select taxa with specific adaptations for success in this niche. However, biotic stress, especially from plant disease, could disrupt this environment in ways that alter the resulting phyllosphere community, with potential consequences for plant and human health. Additionally, plant disease resistance, through both broad (pattern-triggered immunity) and specific (effector-triggered immunity) resistance, could affect non-pathogenic communities directly or indirectly via effects on disease progression. Here, we tested how transgenic ETI and PTI resistance genes affected the phyllosphere communities of tomato plants in the face of infection byXanthomonas perforansand the resulting bacterial spot disease. We found that the expression of theBs2transgene (ETI) had major effects on phyllosphere communities, while the EFR (PTI) transgene did not. The effect of theBs2resistance gene could be largely attributed to the change in disease symptoms. Diseased leaves harbored reduced bacterial diversity and reductions in major phyllosphere inhabitants (e.g.SphinogmonasandMethylobacterium), while a limited number of bacterial genera showed increased relative abundance on diseased leaves. These results suggest that phyllosphere communities are sensitive to the direct and indirect effects of plant disease and resistance, and the consequences of these shifts for plant and human health deserve further investigation.
Is thermal aptitude a pivotal driver in the establishment of recentPuccinia striiformisf. sp.triticilineages in Europe?
Authors: Meyer Kevin JG , Leconte Marc , Vidal Tiphaine , Goyeau Henriette , Suffert Frédéric 
Published: August 2023

AbstractIn the context of global warming, it is crucial to focus on the effects of temperature on the emergence of new lineages of endemic pathogen species, such asPuccinia striiformisf. sp.tritici(Pst) the causal agent of yellow rust on wheat. We characterized the thermal aptitude of representative isolates from the most recent common EuropeanPstraces. We assessed two key aggressiveness components – infection efficiency (IE) and latency period (LP) – under warm and cold thermal regimes, comparing 10Pstisolates collected from 2010 to 2020 with three “old” reference isolates. The significant differences observed suggest that this species has the potential to adapt to temperature changes, but that such adaptation probably did not drive the establishment of the most recent races and the dominant ‘Warrior’ and ‘Warrior(-)’ they succeeded. These races display “generalist” behavior with respect to temperature, with ‘Warrior(-)’ showing no more aggressiveness than the races replaced since the 1990s. The differences in competitive success between emergingPstlineages are probably due to the deployment of resistance genes in wheat and the advantages of new forms of virulence emerging independently of thermal adaptability. However, variations in thermal adaptability for both aggressiveness components suggested an impact of geographic origin within the ‘Warrior’ and ‘Warrior(-)’ races, as previously reported for the “old” reference isolates. Furthermore, the independence of thermal adaptability established for IE and LP implies that the effects of temperature may depend on the stage of the epidemic (early or late), potentially modifying seasonal dynamics.