bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic analysis ofMycobacterium bovisReveals Evidence Of Animal And Zoonotic Tuberculosis Transmission Between Morocco And European Countries
Authors: Yahyaoui Azami Hind , Perea Claudia , Stuber Tod , Bouslikhane Mohammed , Berrada Jaouad , Aboukhassib Hamid , Allepuz Palau Alberto Oscar , Reis Ana C. , Cunha Mónica V. , Thacker Tyler C , Robbe-Austerman Suelee , Salvador Liliana C. M. , Quinn Frederick 
Published: February 2024

AbstractLivestock production is a fundamental pillar of the Moroccan economy. Infectious diseases of cattle and other species represent a significant threat to the livestock industry, animal health, and food safety and security. Bovine tuberculosis (bTB), mainly caused byMycobacterium bovis(M. bovis), generates considerable direct and indirect economic losses, in addition to the unknown human health burden caused by zoonotic transmission. Previous studies have suggested likelyM. bovistransmission links between Morocco and Southern Europe, however, limitations inherent with the methods used prevented more definitive conclusions from being drawn. In this study, we employed whole genome sequencing analysis of a large set ofM. bovisisolates to better define the phylogenetic links between strains from Morocco and neighboring countries. A total of 780M. bovissequences representing 36 countries were included in the study. The results of SNP analysis showed a close genetic relationship betweenM. bovisfrom Morocco and each of Spain, France, Portugal and Germany, this is supported by animal trade between Morocco and these countries, in addition to the important human migration from Morocco to Europe and North America.Regarding zoonotic tuberculosis (TB) transmission, we were able to find genetic links betweenM. bovisisolates from cattle in Morocco and humans in Italy, Germany, and the UK. These results support our hypothesis of significant transmission ofM. bovisfrom cattle to humans, which calls for further investigations of zoonotic TB transmission in Morocco and in other countries.The fact that noM. bovissequences from North Africa in the present database were classified as AF1 or AF2 clonal complexes suggests that the Sahara might play a role in preventingM. bovistransmission between North Africa and Sub-Saharan Africa. Our study benefits from a large sample size and a rich dataset that includes sequences from cattle, wildlife, and humans from Morocco and neighboring countries, enabling the delineation ofM. bovistransmission routes within the animal-human interface.
What “unexplored” means: Mapping undersampled regions in natural history collections
Authors: Ball Laymon , Bedoya Ana M. , Machado Sheila Rodriguez , Paredes-Burneo Diego , Rutledge Samantha , Boyd David , Vander Pluym David , Babb-Biernacki Spenser , Chipps Austin S. , Ozturk Rafet C. , Terzi Yahya , Chakrabarty Prosanta 
Published: February 2024

AbstractWe examined global records of accessible natural history voucher collections (with publicly available data) for terrestrial and freshwater vascular plants, fungi, freshwater fishes, birds, mammals, and herpetofauna (amphibians and reptiles) and highlight areas of the world that would be considered undersampled and sometimes called “unexplored” (i.e., have relatively low, or no evidence of, past sampling efforts) under typical Western-scientific descriptions. We also question what “unexplored” may actually mean in these contexts and explain how retiring the term in favor of more nuanced phrasing can mitigate future misunderstandings of natural history science.
Human coronavirus 229E infection inactivates pyroptosis executioner gasdermin D but ultimately leads to lytic cell death partly mediated by gasdermin E
Authors: Martiáñez-Vendrell Xavier , Bloeme Jonna , Hutchinson Roy , Guy Coralie , Bowie Andrew , Kikkert Marjolein 
Published: February 2024

AbstractHuman coronavirus 229E (HCoV-229E) is associated with upper respiratory tract infections and causes local respiratory symptoms. It has been reported that HCoV-229E can cause cell death in a variety of cellsin vitro. However, the molecular pathways that lead to virus-induced cell death remain poorly characterized. Here, we show that the main protease (Mpro) of HCoV-229E can cleave the pyroptosis executioner gasdermin D (GSDMD) within its active N-terminal domain at two different sites (Q29 and Q193) to generate fragments unable to cause pyroptosis. Despite GSDMD cleavage by HCoV-229E Mpro, we show that HCoV-229E infection leads to lytic cell death. We further demonstrate that virus-induced lytic cell death is partially dependent on the activation of caspases-3 and -8. Interestingly, inhibition of caspases does not only reduce lytic cell death upon infection, but also sustains the release of virus particles over time, which suggests that caspase-mediated cell death is a mechanism to limit virus replication and spread. Finally, we show that pyroptosis is partially dependent on another gasdermin family member, gasdermin E (GSDME). During HCoV-229E infection, GSDME is cleaved to yield its N-terminal pore-forming domain (p30). Accordingly, GSDME knockout cells show a significant decrease in lytic cell death upon virus, whereas this is not the case for GSDMD knockout cells, which aligns with the observation that GSDMD is also inactivated by caspase-3 during infection. These results suggest that GSDMD is inactivated during HCoV-229E infection, and point to GSDME as an important player in the execution of virus-induced cell death.ImportanceRecently, it has been shown that the Mpros of coronaviruses possess accessory functions other than their main role in the proteolytic processing of the viral polyproteins. Although the SARS-CoV-2 outbreak has fuelled the discovery of host cellular substrates of SARS-CoV-2 Mpro, less is known about the interplay of less pathogenic human coronavirus Mpros with host proteins. We demonstrate that HCoV-229E Mpro cleaves GSDMD at two sites within its pore-forming domain, which disrupts GSDMD-mediated pyroptosis. These results point to a new strategy for HCoV-229E to escape the host antiviral response. Additionally, we show that GSDME contributes to virus-induced lytic cell death upon activation by caspase-3, shedding light on a previously undescribed cell death mechanism occurring in HCoV-229E infected cells.
Iguanas from above: Citizen scientists provide reliable counts of endangered Galápagos marine iguanas from drone imagery
Authors: Varela-Jaramillo Andrea , Winkelmann Christian , Rivas-Torres Gonzalo , Guayasamin Juan M. , Steinfartz Sebastian , MacLeod Amy 
Published: February 2024

AbstractPopulation surveys are vital for wildlife management, yet traditional methods often demand excessive time and resources, leading to data gaps for many species. Modern technologies such as drones can facilitate field surveys but may also increase data analysis challenges. Citizen Science (CS) can address this issue by engaging non-specialists for data collection and analysis. We evaluated CS for population monitoring using the endangered Galápagos marine iguana as a case study, assessing online volunteers’ ability to detect and count animals in aerial images. Comparing against a Gold Standard dataset of expert counts in 4345 images, we explored optimal aggregation methods from CS inputs, considering image quality and filtering data from infrequent and anonymous participants. During three phases of our project — hosted on the Zooniverse platform — over 13,000 volunteers made 1,375,201 classifications from 57,838 aerial images; each being independently classified 20 (phases 1 & 2) or 30 (phase 3) times. Volunteers achieved 68% to 94% accuracy in detecting iguanas, with more false negatives than false positives. Image quality strongly influenced accuracy; by excluding data from suboptimal pilot-phase images, volunteers counted with 90% to 92% of accuracy. For detecting presence or absence of iguanas, the commonly used ‘majority vote’ aggregation approach (where the answer selected is that given by the majority of individual inputs) produced less accurate results than when a minimum threshold of five (from the 20/30 independent classifications) was used. For counting iguanas, HDBSCAN clustering yielded the best results. Excluding inputs from anonymous and inexperienced volunteers decreased accuracy. We conclude that online volunteers can accurately identify and count marine iguanas from drone images, though a tendency to underestimate warrants further consideration. CS-based data analysis is faster than manual counting but still resource-intensive, underscoring the need to develop a Machine Learning approach.
Polygenic basis of Bt Cry resistance evolution in wildHelicoverpa zea
Authors: Taylor Katherine L , Quackenbush Jane , Lamberty Cara , Hamby Kelly A , Fritz Megan L 
Published: February 2024

AbstractStrong and shifting selective pressures of the anthropocene are rapidly shaping phenomes and genomes of organisms worldwide. One major selective force on insect genomes is crops expressing pesticidal proteins fromBacillus thuringiensis(Bt). Here we characterize a rapid response to selection by Bt crops in a major crop pest,Helicoverpa zea. We reveal the polygenic architecture of Bt resistance evolution inH. zeaand identify multiple genomic regions underlying this trait. In the genomic region of largest effect, we identified a gene cluster amplification, where resistant individuals showed variation in copy number for multiple genes. Signals of this amplification increased over time, consistent with the history of field-evolved Bt resistance evolution. Modern wild populations from disparate geographical regions are positive for this variant at high, but not fixed, allele frequencies. We also detected selection against single copy variants at this locus in wildH. zeacollected from Bt expressing plants, further supporting its role in resistance. Seven trypsin genes were present in this genomic region and all appeared to be significantly upregulated in Bt resistantH. zea. Biochemically inhibiting trypsin activity decreasedH. zea’s tolerance to Bt. These findings characterize rapid genome evolution in a major crop pest following anthropogenic selection and highlight the role that gene copy number variants can have in rapid evolutionary responses.
Brain activation during the N-back working memory task in individuals with spinal cord injury: a functional near-infrared spectroscopy study
Authors: Chen Donna Y. , Di Xin , Amaya Nayyar , Sun Hai , Pal Saikat , Biswal Bharat B. 
Published: February 2024

AbstractCognitive impairments have frequently been reported in individuals with spinal cord injury (SCI) across different domains such as working memory, attention, and executive function. The mechanism of cognitive impairment after SCI is not well understood due to the heterogeneity of SCI sample populations, and may possibly be due to factors such as cardiovascular dysfunction, concomitant traumatic brain injury (TBI), hypoxia, sleep disorders, and body temperature dysregulation. In this study, we implement the Neuropsychiatric Unit Cognitive Assessment Tool (NUCOG) to assess cognitive differences between individuals with SCI and age-matched able-bodied (AB) controls. We then use an N-back working memory task and functional near-infrared spectroscopy (fNIRS) to elucidate the neurovascular correlates of cognitive function in individuals with SCI. We observed significant differences between the SCI and AB groups on measures of executive function on the NUCOG test. On the N-back task, across the three levels of difficulty: 0-back, 2-back, and 3-back, no significant differences were observed between the SCI and AB group; however, both groups performed worse as the level of difficulty increased. Although there were no significant differences in N-back performance scores between the two groups, functional brain hemodynamic activity differences were observed between the SCI and AB groups, with the SCI group exhibiting higher maximum oxygenated hemoglobin concentration in the right inferior parietal lobe. These findings support the use of fNIRS to study cognitive function in individuals with SCI and may provide a useful tool during rehabilitation to obtain quantitative functional brain activity metrics.
The Mouse Inferior Colliculus Responds Preferentially to Non-Ultrasonic Vocalizations
Authors: Tehrani Mahtab , Shanbhag Sharad , Huyck Julia J. , Patel Rahi , Kazimiersky Diana , Wenstrup Jeffrey J. 
Published: February 2024

ABSTRACTThe inferior colliculus (IC), the midbrain auditory integration center, analyzes information about social vocalizations and provides substrates for higher level processing of vocal signals. We used multi-channel recordings to characterize and localize responses to social vocalizations and synthetic stimuli within the IC of female and male mice, both urethane-anesthetized and unanesthetized. We compared responses to ultrasonic vocalizations (USVs) with other vocalizations in the mouse repertoire and related vocal responses to frequency tuning, IC subdivisions, and sex. Responses to lower frequency, broadband social vocalizations were widespread in IC, well represented throughout the tonotopic axis, across subdivisions, and in both sexes. Responses to USVs were much more limited. Although we observed some differences in tonal and vocal responses by sex and subdivision, representations of vocal responses by sex and subdivision were largely the same. For most units, responses to vocal signals occurred only when frequency response areas overlapped with spectra of the vocal signals. Since tuning to frequencies contained within the highest frequency USVs is limited (< 15% of IC units), responses to these vocalizations are correspondingly limited (< 5% of sound-responsive units). These results highlight a paradox of USV processing in some rodents: although USVs are the most abundant social vocalization, their representation and the representation of corresponding frequencies is less than lower frequency social vocalizations. We interpret this paradox in light of observations suggesting that USVs with lower frequency elements (<50 kHz) are associated with increased emotional intensity and engage a larger population of neurons in the mouse auditory system.SIGNIFICANCE STATEMENTThe inferior colliculus (IC) integrates multiple inputs to analyze information about social vocalizations. In mice, we show that the most common type of social vocalization, the ultrasonic vocalization or USV, was poorly represented in IC compared to lower frequency vocalizations. For most neurons, responses to vocal signals occurred only when frequency response areas overlapped with vocalization spectra. These results highlight a paradox of USV processing in some rodent auditory systems: although USVs are the most abundant social vocalization, their representation and representation of corresponding frequencies is less than lower frequency social vocalizations. These results suggest that USVs with lower frequency elements (<50 kHz)—associated with increased emotional intensity—will engage a larger population of neurons in the mouse auditory system.
A Composite Biomarker Signature of Type 1 Diabetes Risk Identified via Augmentation of Parallel Multi-Omics Data from a Small Cohort
Authors: Alcazar Oscar , Chuang Sung-Ting , Ren Gang , Ogihara Mitsunori , Webb-Robertson Bobbie-Jo M. , Nakayasu Ernesto S. , Buchwald Peter , Abdulreda Midhat H. 
Published: February 2024

ABSTRACTBackgroundBiomarkers of early pathogenesis of type 1 diabetes (T1D) are crucial to enable effective prevention measures in at-risk populations before significant damage occurs to their insulin producing beta-cell mass. We recently introduced the concept of integrated parallel multi-omics and employed a novel data augmentation approach which identified promising candidate biomarkers from a small cohort of high-risk T1D subjects. We now validate selected biomarkers to generate a potential composite signature of T1D riskMethodsTwelve candidate biomarkers, which were identified in the augmented data and selected based on their fold-change relative to healthy controls and cross-reference to proteomics data previously obtained in the expansive TEDDY and DAISY cohorts, were measured in the original samples by ELISAResultsAll 12 biomarkers had established connections with lipid/lipoprotein metabolism, immune function, inflammation, and diabetes, but only 7 were found to be markedly changed in the high-risk subjects compared to the healthy controls: ApoC1 and PON1 were reduced while CETP, CD36, FGFR1, IGHM, PCSK9, SOD1, and VCAM1 were elevatedConclusionsResults further highlight the promise of our data augmentation approach in unmasking important patterns and pathologically significant features in parallel multi-omics datasets obtained from small sample cohorts to facilitate the identification of promising candidate T1D biomarkers for downstream validation. They also support the potential utility of a composite biomarker signature of T1D risk characterized by the changes in the above markers.
Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy
Authors: Maurer Katie , Park Cameron Y. , Mani Shouvik , Borji Mehdi , Penter Livius , Jin Yinuo , Zhang Jia Yi , Shin Crystal , Brenner James R. , Southard Jackson , Krishna Sachi , Lu Wesley , Lyu Haoxiang , Abbondanza Domenic , Mangum Chanell , Olsen Lars Rønn , Neuberg Donna S. , Bachireddy Pavan , Farhi Samouil L. , Li Shuqiang , Livak Kenneth J. , Ritz Jerome , Soiffer Robert J. , Wu Catherine J. , Azizi Elham 
Published: February 2024

SummaryUnderstanding how intra-tumoral immune populations coordinate to generate anti-tumor responses following therapy can guide precise treatment prioritization. We performed systematic dissection of an established adoptive cellular therapy, donor lymphocyte infusion (DLI), by analyzing 348,905 single-cell transcriptomes from 74 longitudinal bone-marrow samples of 25 patients with relapsed myeloid leukemia; a subset was evaluated by protein-based spatial analysis. In acute myelogenous leukemia (AML) responders, diverse immune cell types within the bone-marrow microenvironment (BME) were predicted to interact with a clonally expanded population ofZNF683+GZMB+CD8+ cytotoxic T lymphocytes (CTLs) which demonstratedin vitrospecificity for autologous leukemia. This population, originating predominantly from the DLI product, expanded concurrently with NK and B cells. AML nonresponder BME revealed a paucity of crosstalk and elevatedTIGITexpression in CD8+ CTLs. Our study highlights recipient BME differences as a key determinant of effective anti-leukemia response and opens new opportunities to modulate cell-based leukemia-directed therapy.
Structural characterization of the ACDC domain from ApiAP2 proteins of the malaria parasite
Authors: Le Berre Marine , Tubiana Thibault , Reuterswärd Waldner Philippa , Lazar Noureddine , Li de la Sierra Ines , Santos Joana Mendonca , Llinás Manuel , Nessler Sylvie 
Published: February 2024

AbstractThe Apicomplexan AP2 (ApiAP2) proteins are the best characterized family of DNA-binding proteins in the malaria parasite. Apart from the AP2 DNA-binding domain, there is little sequence similarity between ApiAP2 proteins and no other functional domains have been extensively characterized. One protein domain, which is present in a subset of the ApiAP2 proteins, is the conserved AP2-coincident domain mostly at the C-terminus (ACDC domain). Here we solved for the first time the crystal structure of the ACDC domain from two distinctPlasmodium falciparumApiAP2 proteins and one orthologue fromP. vivax, revealing a non-canonical four-helix bundle. Despite little sequence conservation between the ACDC domains from the two proteins, the structures are remarkably similar and do not resemble that of any other known protein domains. Due to their unique protein architecture and lack of homologues in the human genome, we performedin silicodocking calculations against a library of known antimalarial compounds and we identified a small molecule that can potentially bind to any Apicomplexan ACDC domain within a pocket highly conserved amongst ApiAP2 proteins. Inhibitors based on this compound would disrupt the function of the ACDC domain and thus of the ApiAP2 proteins containing it, providing a new therapeutic window for targeting the malaria parasite and other Apicomplexans.
Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles
Authors: Gable Simone M. , Bushroe Nicholas , Mendez Jasmine , Wilson Adam , Pinto Brendan , Gamble Tony , Tollis Marc 
Published: February 2024

AbstractTransposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.
The contribution of movement to social network structure and spreading dynamics under simple and complex transmission
Authors: Chimento Michael , Farine Damien R. 
Published: February 2024

AbstractThe structure of social networks fundamentally influences spreading dynamics. In general, the more contact between individuals, the more opportunity there is for the transmission of information or disease to take place. Yet, contact between individuals, and any resulting transmission events, are determined by a combination of spatial (where individuals choose to move) and social rules (who they choose to interact with or learn from). Here we examine the effect of the social-spatial interface on spreading dynamics using a simulation model. We quantify the relative effects of different movement rules (localized, semi-localized, nomadic, and resource-based movement) and social transmission rules (simple transmission, anti-conformity, proportional, conformity, and threshold rules) to both the structure of social networks and spread of a novel behaviour. Localized movement created weakly connected sparse networks, nomadic movement created weakly connected dense networks, and resource-based movement generated strongly connected modular networks. The resulting rate of spreading varied with different combinations of movement and transmission rules, but— importantly—the relative rankings of transmission rules changed when running simulations on static versus dynamic representations of networks. Our results emphasize that individual-level social and spatial behaviours influence emergent network structure, and are of particular consequence for the spread of information under complex transmission rules.