bluuebunny/crossref_metadata_2025_split huggingface dataset:
The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance inEnterobacterales
Authors: Cartagena Alexis Jaramillo , Taylor Kyra L. , Smith Joshua T. , Manson Abigail L. , Pierce Virginia M. , Earl Ashlee M. , Bhattacharyya Roby P. 
Published: May 2023

AbstractCarbapenem-resistantEnterobacterales(CRE) are important pathogens that can develop resistance via multiple molecular mechanisms, including hydrolysis or reduced antibiotic influx. Identifying these mechanisms can improve pathogen surveillance, infection control, and patient care. We investigated how resistance mechanisms influence the carbapenem inoculum effect (IE), a phenomenon where inoculum size affects antimicrobial susceptibility testing (AST). We demonstrated that seven different carbapenemases impart a meropenem IE inEscherichia coli. Across 110 clinical CRE isolates, the carbapenem IE strictly depended on resistance mechanism: all carbapenemase-producing CRE (CP-CRE) exhibited a strong IE, whereas porin-deficient CRE displayed none. Concerningly, 50% and 24% of CP-CRE isolates changed susceptibility classification to meropenem and ertapenem, respectively, across the allowable inoculum range in clinical guidelines. The meropenem IE, and the ratio of ertapenem to meropenem minimal inhibitory concentration (MIC) at standard inoculum, reliably identified CP-CRE. Understanding how resistance mechanisms affect AST could improve diagnosis and guide therapies for CRE infections.
Enhanced Annotation of CD45RA to Distinguish T cell Subsets in Single Cell RNA-seq via Machine Learning
Authors: Ran Ran , Brubaker Douglas K. 
Published: May 2023

AbstractT cell heterogeneity presents a challenge for accurate cell identification, understanding their inherent plasticity, and characterizing their critical role in adaptive immunity. Immunologists have traditionally employed techniques such as flow cytometry to identify T cell subtypes based on a well-established set of surface protein markers. With the advent of single-cell RNA sequencing (scRNA-seq), researchers can now investigate the gene expression profiles of these surface proteins at the single-cell level. The insights gleaned from these profiles offer valuable clues and a deeper understanding of cell identity. However, CD45RA, the isoform of CD45 which distinguish between naïve/central memory T cells and effector memory/effector memory cells re-expressing CD45RA T cells, cannot be well profiled by scRNA-seq due to the difficulty in mapping short reads to genes. In order to facilitate cell type annotation in T cell scRNA-seq analysis, we employed machine learning and trained a CD45RA+/-classifier on single-cell mRNA count data annotated with known CD45RA antibody levels provided by cellular indexing of transcriptomes and epitopes sequencing (CITE-seq) data. Among all algorithms we tested, the trained support vector machine (SVM) with a radial basis function (RBF) kernel with optimized hyperparameters achieved a 99.96% accuracy on an unseen dataset. The multilayer Perceptron (MLP) classifier, the second most predictive method overall, also achieved a decent accuracy of 99.74%. Our simple yet robust machine learning approach provides a valid inference on the CD45RA level, assisting the cell identity annotation and further exploring the heterogeneity within human T cells.
On the cusp of adaptive change: the hierarchical radiation of phyllostomid bats
Authors: Grossnickle David M. , Sadier Alexa , Patterson Edward , Cortés-Viruet Nashaly N. , Rivera Stephanie Jimenez , Sears Karen E. , Santana Sharlene E. 
Published: May 2023

ABSTRACTAdaptive radiations are bursts in biodiversity that lead to the origin of new evolutionary lineages and phenotypes. However, adaptive radiations typically occur over millions of years and it is unclear how the macroevolutionary dynamics that underpin them vary through time and among groups of organisms. Phyllostomid bats radiated extensively for diverse diets –from insects to vertebrates, fruit, nectar, and blood– and we use their molars as a model system to examine the dynamics of adaptive radiations. Three-dimensional shape analyses of lower molars of Noctilionoidea (Phyllostomidae and close relatives) indicate that different diet groups exhibit distinct morphotypes. Comparative analyses further reveal that phyllostomids are a striking example of a hierarchical radiation; their initial, higher-level diversification involved an ‘early burst’ in molar morphological disparity as lineages invaded new diet-affiliated adaptive zones, followed by subsequent lower-level diversifications within adaptive zones involving less dramatic morphological changes. We posit that strong selective pressures related to initial shifts to derived diets may have freed molars from morpho-functional constraints associated with the ancestral molar morphotype. Then, lineages with derived diets (frugivores and nectarivores) diversified considerably within broad adaptive zones, likely reflecting finer-scale niche partitioning. The observed early burst pattern is only evident when examining molar traits that are strongly linked to diet, highlighting the importance of ecomorphological traits in comparative studies. Our results support the hypothesis that adaptive radiations are commonly hierarchical and involve different tempos and modes at different phylogenetic scales, with early bursts being more common at broader scales.SIGNIFICANCE STATEMENTMany groups of organisms are exceptionally diverse in their ecology, morphology, and number of species. But there is debate as to whether these groups commonly achieved this diversity through ‘bursts’ in diversification early in their history. Phyllostomid bats are one of the most ecologically diverse mammalian families and a classic example of an adaptive radiation. We use their molar shapes, which correlate with diet, as a model for examining macroevolutionary patterns during diversifications. We find that phyllostomids experienced a two-step process of diversification; the first step involved a rapid burst, whereas the second involved finer-scale changes as lineages filled ecological niches. We posit that this is a common, yet underappreciated, pattern during the early histories of many diverse clades.
Spp1 secreted by macrophages impairs osteogenic ability of Ctsk+Fmod+periosteal cells in jaw bone
Authors: Yi Zumu , Liu Yeyu , Wang Jing , Hu Chen , Man Yi 
Published: May 2023

AbstractPeriosteum, which covers the surface of most bones, mediates bone regeneration through endochondral ossification during fracture repair and intramembranous ossification under steady state. Periosteal cells (PCs) of jaw bones are different from those of long bones in phenotypic characteristics and functions. So far, the role of periosteum in jaw bones during bone grafting remain unclarified. Here we propose a subperiosteal bone grafting model based on the clinical procedures. By integrating single-cell RNA sequencing (scRNA-seq) and spatial transcriptomic (ST), we found a functional Ctsk+Fmod+subset of PCs in jaw bones. The Ctsk+Fmod+PCs had the potential of multi-directional differentiation. Furthermore, Spp1 secreted by macrophages could impair the osteogenic capacity of Ctsk+Fmod+PCs, which could be partly rescued by blocking Spp1. The identification of this Ctsk+Fmod+subclusters, which shows osteoprogenitor characteristics and close interaction with macrophages, reveals the heterogeneity of periosteal cells in jaw bones, and may provide target of intervention to improve osteogenesis during bone augmentation surgery.
The unexpected loss of the “hunger hormone” ghrelin in true passerines: A game changer in migration physiology
Authors: Prost Stefan , Elbers Jean P. , Slezacek Julia , Fuselli Silvia , Smith Steve , Fusani Leonida 
Published: May 2023

AbstractMigratory birds must accumulate large amounts of fat prior to migration to sustain long flights. In passerines, the small body size limits the amount of energy stores that can be transported and therefore birds undergo cycles of extreme fattening and rapid exhaustion of reserves. Research on these physiological adaptations was rattled by the discovery that birds have lost the main vertebrate regulator of fat deposition,leptin. Recent studies have thus focused onghrelin, known as the “hunger hormone”, a peptide secreted by the gastrointestinal tract to regulate food intake, body mass, and other important functions in vertebrates. Studies on domestic species showed that in birdsghrelinhas effects opposite to those described in mammals, such as inhibiting instead of promoting food intake. Furthermore, a series of recent studies have shown thatghrelinadministration influences migratory behaviour in passerine birds, suggesting an important role of this hormone in bird migration. However, using comparative genomic analyses we show thatghrelinhas been lost in the largest avian taxon Eupasseres, after the basic split from Acanthisitti about 50 million years ago. Eupasserines, also known as True passerines, include all but two of the ca. 10,000 known passerine species. We further found that theghrelinreceptor (growth hormone secretagogue receptor, GHS-R) is still conserved in passerine birds, as indicated by sites under purifying selection and in line with the effects ofghrelinadministration. Thus,ghrelinadds to a list of hormones highly conserved in vertebrates that have lost their main functions in specific taxa. The maintenance of a functional receptor system, however, suggests that in eupasserine birds another ligand has replacedghrelin, perhaps to bypass the feedback system that would hinder large pre-migratory accumulation of subcutaneous fat.
De novomotor learning creates structure in neural activity space that shapes adaptation
Authors: Chang Joanna C. , Perich Matthew G. , Miller Lee E. , Gallego Juan A. , Clopath Claudia 
Published: May 2023

AbstractAnimals can quickly adapt learned movements in response to external perturbations. Motor adaptation is likely influenced by an animal’s existing movement repertoire, but the nature of this influence is unclear. Long-term learning causes lasting changes in neural connectivity which determine the activity patterns that can be produced. Here, we sought to understand how a neural population’s activity repertoire, acquired through long-term learning, affects short-term adaptation by modeling motor cortical neural population dynamics duringde novolearning and subsequent adaptation using recurrent neural networks. We trained these networks on different motor repertoires comprising varying numbers of movements. Networks with multiple movements had more constrained and robust dynamics, which were associated with more defined neural ‘structure’—organization created by the neural population activity patterns corresponding to each movement. This structure facilitated adaptation, but only when small changes in motor output were required, and when the structure of the network inputs, the neural activity space, and the perturbation were congruent. These results highlight trade-offs in skill acquisition and demonstrate how prior experience and external cues during learning can shape the geometrical properties of neural population activity as well as subsequent adaptation.
Accelerated prime-and-trap vaccine regimen in mice using repRNA-based CSP malaria vaccine
Authors: MacMillen Zachary , Hatzakis Kiara , Simpson Adrian , Shears Melanie J. , Watson Felicia , Erasmus Jesse H. , Khandhar Amit P. , Wilder Brandon , Murphy Sean C. , Reed Steven G. , Davie James W. , Avril Marion 
Published: May 2023

ABSTRACTMalaria, caused byPlasmodiumparasites, remains one of the most devastating infectious diseases worldwide, despite control efforts that have lowered morbidity and mortality. The onlyP. falciparumvaccine candidates to show field efficacy are those targeting the asymptomatic pre-erythrocytic (PE) stages of infection. The subunit (SU) RTS,S/AS01 vaccine, the only licensed malaria vaccine to date, is only modestly effective against clinical malaria. Both RTS,S/AS01 and the SU R21 vaccine candidate target the PE sporozoite (spz) circumsporozoite (CS) protein. These candidates elicit high-titer antibodies that provide short-term protection from disease, but do not induce the liver-resident memory CD8+T cells (Trm) that confer strong PE immunity and long-term protection. In contrast, whole-organism (WO) vaccines, employing for example radiation-attenuated spz (RAS), elicit both high antibody titers and Trm, and have achieved high levels of sterilizing protection. However, they require multiple intravenous (IV) doses, which must be administered at intervals of several weeks, complicating mass administration in the field. Moreover, the quantities of spz required present production difficulties. To reduce reliance on WO while maintaining protection via both antibodies and Trm responses, we have developed an accelerated vaccination regimen that combines two distinct agents in a prime-and-trap strategy. While the priming dose is a self-replicating RNA encodingP. yoeliiCS protein, delivered via an advanced cationic nanocarrier (LIONTM), the trapping dose consists of WO RAS. This accelerated regime confers sterile protection in theP. yoeliimouse model of malaria. Our approach presents a clear path to late-stage preclinical and clinical testing of dose-sparing, same-day regimens that can confer sterilizing protection against malaria.
Functional Subtypes of Synaptic Dynamics in Mouse and Human
Authors: Beninger John , Rossbroich Julian , Tóth Katalin , Naud Richard 
Published: May 2023

AbstractSynapses show preferential responses to particular temporal patterns of activity. Across individual synapses, there is a large degree of response heterogeneity that is informally or tacitly separated into classes, and typically only two: facilitating and depressing short-term plasticity. Here we combined a kernel-based model and machine learning techniques to infer the number and the characteristics of functionally distinct subtypes of short-term synaptic dynamics in a large dataset of glutamatergic cortical connections. To this end, we took two independent approaches. First, we used unsupervised techniques to group similar synapses into clusters. Second, we used supervised prediction of cell subclasses to reveal features of synaptic dynamics that characterized cellular genetic profiles. In rodent data, we found five clusters with a remarkable degree of convergence with the transgenic-associated subtypes. Two of these clusters corresponded to different degrees of facilitation, two corresponded to depression with different degrees of variability and one corresponded to depression-then-facilitation. Strikingly, the application of the same clustering method in human data inferred highly similar clusters to those observed in rodents, supportive of a stable clustering procedure and suggesting a homology of functional subtypes across species. This nuanced dictionary of functional subtypes shapes the heterogeneity of cortical synaptic dynamics and provides a lens into the basic motifs of information transmission in the brain.
Embryonic organizer specification in the mud snailIlyanassa obsoletadepends on intercellular signaling
Authors: Wandelt Jessica E. , Nakamoto Ayaki , Goulding Morgan Q , Nagy Lisa M. 
Published: May 2023

ABSTRACTIn early embryos of the neogastropodIlyanassa obsoleta, cytoplasmic segregation of a polar lobe is required for establishment of the D macromere, empowering its great-granddaughter macromere 3D to act as a single-celled organizer that induces body patterning along the secondary axis. We present evidence that polar lobe inheritance is not sufficient to specify 3D potential, but rather makes the D macromere lineage responsive to some intercellular signal(s) required for activating the special properties of 3D. Experimental removal of micromeres results in loss of organizer-linked MAPK activation, complete and specific defects of organizer-dependent larval organs, and progressive cell cycle retardation leading to equalization of the normally accelerated division schedule of 3D. Ablation of the second-quartet micromere 2d greatly potentiates the effects of first-quartet micromere ablation. Our findings link 3D establishment inI. obsoletato the putative ancestral spiralian mechanism in which a signal from micromeres leads to specification of 3D among four initially equivalent macromeres.Summary StatementCell ablation experiments on embryos of the snailIlyanassareveal that specification of the organizer cell 3D depends on cell-extrinsic cues as well as polar lobe inheritance.
Generation of aPlasmodium falciparumreporter line for studies of parasite biology throughout the life cycle
Authors: Suárez-Cortés Pablo , Costa Giulia , Andres Manuela , Eyermann Daniel , Kreschel Cornelia , Spohr Liane , Goosmann Christian , Brinkmann Volker , Levashina Elena A. 
Published: May 2023

AbstractFluorescence reporter strains of human malaria parasites are powerful tools to study the interaction of the parasites with both human and mosquito hosts. However, low fluorescence intensity in transmission-relevant parasite stages and the choice of insertion loci that cause parasite developmental defects in the mosquito largely limits usefulness of currently available lines. To overcome these limitations, we used a CRISPR-Cas9-mediated approach to generatePfOBC13GFP, a novel selection marker-free reporter parasite in the background of the African NF54Plasmodium falciparumline. As docking site, we selected theOBC13locus that is dispensable for asexual and sexual developmentin vitro.PfOBC13GFPparasites encode GFP flanked byhsp70UTRs that drive strong fluorescence reporter expression throughout blood and mosquito stages, enabling parasite detection by such high throughput methods as flow cytometry. When compared to the parental line,PfOBC13GFPparasites showed normal development during blood and mosquito stages, and they efficiently infected the main African vectorAnopheles coluzzii,overcoming one of the limitations of the previously developed fluorescent reporter lines based on thePfs47locus.PfOBC13GFPconstitutes a potent tool enabling host-pathogen studies throughoutPlasmodiumlife cycle.ImportanceFluorescence reporter strains have been very useful in malaria research, however, up to date they had limitations in mosquito infectivity and fluorescence intensity. Here we report the generation ofPfOBC13GFP, a new fluorescent parasite strain of the human malaria parasiteP. falciparum.PfOBC13GFPparasites are highly fluorescent throughout the life cycle, making them an ideal tool for the study the parasite progression through blood and mosquito stages. They efficiently infect the African mosquitovector A. coluzzii, allowing the study of this African parasite in its biological background. Moreover, strong parasite fluorescence enables flow cytometry and live microscopy characterization of all parasite stages, especially those involved in transmission.
Transposon dynamics in the emerging oilseed cropThlaspi arvense
Authors: Contreras-Garrido Adrián , Galanti Dario , Movilli Andrea , Becker Claude , Bossdorf Oliver , Drost Hajk-Georg , Weigel Detlef 
Published: May 2023

AbstractGenome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspecific diversity of TE polymorphisms is shaping the broad geographic success and adaptation capacity of the emerging oil cropThlaspi arvense. We achieved this by classifying the TE inventory of this species based on a high-quality genome assembly, age estimation of retrotransposon TE families and a comprehensive assessment of their mobilization potential. Our survey of TE insertion polymorphisms (TIPs) captured 280 accessions from 12 regions across the Northern hemisphere. We quantified over 90,000 TIPs, with their distribution mirroring genetic differentiation as measured by single nucleotide polymorphisms (SNPs). The number and types of mobile TE families vary substantially across populations, but there are also shared patterns common to all accessions. We found that Ty3/Athila elements are the main drivers of TE diversity inT. arvensepopulations, while a single Ty1/Alesia lineage might be particularly important for molding transcriptome divergence. We further observed that the number of retrotransposon TIPs is associated with variation at genes related to epigenetic regulation while DNA transposons are associated with variation at a Heat Shock Protein (HSP19). We propose that the high rate of mobilization activity can be harnessed for targeted gene expression diversification, which may ultimately present a toolbox for the potential use of transposition in breeding and domestication ofT. arvense.
All-optical interrogation of brain-wide activity in freely swimming larval zebrafish
Authors: Chai Yuming , Qi Kexin , Wu Yubin , Li Daguang , Tan Guodong , Guo Yuqi , Chu Jun , Mu Yu , Shen Chen , Wen Quan 
Published: May 2023

SummaryWe introduce an all-optical technique that enables volumetric imaging of brain-wide calcium activity and targeted optogenetic stimulation of specific brain regions in freely swimming larval zebrafish. The system consists of three main components: a 3D tracking module, a dual color fluorescence imaging module, and a real-time activity manipulation module. Our approach uses a sensitive genetically encoded calcium indicator in combination with a long Stokes shift red fluorescence protein as a reference channel, allowing the extraction of Ca2+activity from signals contaminated by motion artifacts. The method also incorporates rapid 3D image reconstruction and registration, facilitatingreal-timeselective optogenetic stimulation of different regions of the brain. By demonstrating that selective light activation of the midbrain regions in larval zebrafish could reliably trigger biased turning behavior and changes of brain-wide neural activity, we present a valuable tool for investigating the causal relationship between distributed neural circuit dynamics and naturalistic behavior.HighlightsWe develop an all-optical technique that enables simultaneous whole brain imaging and optogenetic manipulation of selective brain regions in freely behaving larval zebrafish.A combination of a genetically encoded calcium indicator and a long Stokes-shift red fluorescence protein, together with the adaptive filter algorithm, enables us to reliably distinguish calcium activity from motion-induced signal contamination.Rapid 3D image reconstruction and registration enables real-time targeted optogenetic stimulation of distinct brain regions in a freely swimming larval zebrafish.