bluuebunny/crossref_metadata_2025_split huggingface dataset:
An open-source MRI compatible frame for multimodal presurgical mapping in macaque and capuchin monkeys
Authors: Liang Lucy , Zimmermann Rollin Isabela , Alikaya Aydin , Ho Jonathan C. , Santini Tales , Bostan Andreea C. , Schwerdt Helen N. , Stauffer William R. , Ibrahim Tamer S. , Pirondini Elvira , Schaeffer David J. 
Published: February 2024

AbstractHighlights:We present a compact MRI-compatible stereotaxic frame for large nonhuman primates.The design is 3D printable, inexpensive, and matches size of an adult human head.Enabled real-time, accurate, MRI-guided deep-brain viral vector injection.Facilitated multimodal alignment for deep-brain electrophysiology planning.All computer-aided-design files are modularized and publicly available and editable.BackgroundHigh-precision neurosurgical targeting in nonhuman primates (NHPs) often requires presurgical anatomy mapping with noninvasive neuroimaging techniques (MRI, CT, PET), allowing for translation of individual anatomical coordinates to surgical stereotaxic apparatus. Given the varied tissue contrasts that these imaging techniques produce, precise alignment of imaging-based coordinates to surgical apparatus can be cumbersome. MRI-compatible stereotaxis with radiopaque fiducial markers offer a straight-forward and reliable solution, but existing commercial options do not fit in conformal head coils that maximize imaging quality.New methodWe developed a compact MRI-compatible stereotaxis suitable for a variety of NHP species (Macaca mulatta,Macaca fascicularis, andCebus apella) that allows multimodal alignment through technique-specific fiducial markers.Comparison with existing methodsWith the express purpose of compatibility with clinically available MRI, CT, and PET systems, the frame is no larger than a human head, while allowing for imaging NHPs in the supinated position. This design requires no marker implantation, special software, or additional knowledge other than the operation of a common large animal stereotaxis.ResultsWe demonstrated the applicability of this 3D-printable apparatus across a diverse set of experiments requiring presurgical planning: 1) We demonstrate the accuracy of the fiducial system through a within-MRI cannula insertion and subcortical injection of viral vectors. 2) We also demonstrated accuracy of multimodal (MRI and CT) alignment and coordinate transfer to guide a surgical robot electrode implantation for deep-brain electrophysiology.ConclusionsThe computer-aided design files and engineering drawings are publicly available, with the modular design allowing for low cost and manageable manufacturing.
Stochastic regimes can hide the attractors in data, reconstruction algorithms can reveal them
Authors: M. S. Arani Babak , R. Carpenter Stephen , H. van Nes Egbert , A. van de Leemput Ingrid , Xu Chi , G. Lind Pedro , Scheffer Marten 
Published: February 2024

AbstractTipping points and alternative attractors have become an important focus of research and public discussions about the future of climate, ecosystems and societies. However, empirical evidence for the existence of alternative attractors remains scarce. For example, bimodal frequency distributions of state variables may suggest bistability, but can also be due to bimodality in external conditions. Here, we bring a new dimension to the classical arguments on alternative stable states and their resilience showing that the stochastic regime can distort the relationship between the probability distribution of states and the underlying attractors. Simple additive Gaussian white noise produces a one-to-one correspondence between the modes of frequency distributions and alternative stable states. However, for more realistic types of noise, the number and position of modes of the frequency distribution do not necessarily match the equilibria of the underlying deterministic system. We show that data must represent the stochastic regime as thoroughly as possible. When data are adequate then existing methods can be used to determine the nature of the underlying deterministic system and noise simultaneously. This may help resolve the question of whether there are tipping points, but also how realized states of a system are shaped by stochastic forcing vs internal stability properties.Open Research StatementData and MATLAB codes for results reported here are available in the Github repositoryhttps://github.com/mshoja/Reconst(Babak M. S. Arani 2023) The original data source is cited in the text.
Potential of Photoelectric Stimulation with Ultrasmall Carbon Electrode on Neural Tissue: New Directions in Neuromodulation Technology Development
Authors: Chen Keying , Wu Bingchen , Krahe Daniela , Vazquez Alberto , Siegenthaler James R. , Rechenberg Robert , Li Wen , Cui X. Tracy , Kozai Takashi D.Y. 
Published: February 2024

AbstractObjectiveNeuromodulation technologies have gained considerable attention for its clinical potential in treating neurological disorders and their capacity to advance cognition research. Nevertheless, traditional neuromodulation methods such as electrical stimulation and optogenetics manipulation currently experience technical and biological challenges that hinge their therapeutic potential and chronic research applications. Recently, a promising alternative neuromodulation approach based on the photoelectric effect has emerged. This approach is capable of generating electrical pulses when exposed to near-infrared (NIR) light and allows modulation of neuronal activity without the need for genetic alterations. In this study, we investigate a variety of design strategies aimed at enhancing photoelectric stimulation using minimally invasive, ultrasmall, untethered carbon electrodes.ApproachA multiphoton laser was employed as the NIR light source. Benchtop investigations were conducted using a three-electrode setup, and chronopotentiometry was used to record photo-stimulated voltage. Forin vivoevaluation, we used Thy1-GCaMP6s mice with acute implantation of ultrasmall carbon electrodes.Main resultsWe revealed the beneficial effects of high duty-cycle laser scanning and photovoltaic polymer interfaces on the photo-stimulated voltages of ultrasmall carbon electrodes. Additionally, we demonstrated the promising potential of carbon-based diamond electrodes for photoelectric stimulation and examined the application of photoelectric stimulation in precise chemical delivery by loading mesoporous silica nanoparticles (SNPs) co-deposited with polyethylenedioxythiophene (PEDOT).SignificanceThese findings on photoelectric stimulation utilizing ultrasmall carbon electrodes underscore its immense potential for advancing the next generation of neuromodulation technology. This approach offers the opportunity to effectively modulate neural tissue while minimizing invasive implantation-related injuries in freely moving subjects, which hold significant promise for a wide range of applications in neuroscience research and clinical settings.
Structural architecture of a prokaryotic metabolon reveals conserved interfaces mediating multiple protein-protein interactions
Authors: Bhattacharyya Sanchari , Ranganathan Srivastav , Chowdhury Sourav , Adkar Bharat V , Khrapko Mark , Shakhnovich Eugene I 
Published: February 2024

AbstractEnzymes in a pathway often form metabolons through weak protein-protein interactions (PPI) that localize and protect labile metabolites. Due to their transient nature, the structural architecture of these enzyme assemblies has largely remained elusive, thereby limiting our abilities to re-engineer novel metabolic pathways. Here we delineate a complete PPI map of 1225 interactions in theE. coli1-carbon metabolism pathway using bimolecular fluorescence complementation that can capture transient interactionsin vivoand show strong intra- and inter-pathway clusters within the folate and purine biosynthesis pathways. Further, deep scanning mutagenesis experiments along with AlphaFold predictions and meta-dynamics simulations not only reveal interaction interfaces of all PPI in the folate pathway but also uncovers that most proteins use conserved “dedicated” interfaces distant from their active sites to interact with multiple partners. Overall, this study sheds light on the fundamental features of metabolon biophysics and structural aspects of transient binary complexes.Significance statementEnzymes from the same metabolic pathway often form dynamic assemblies called metabolons, which channel metabolites as well as protect labile intermediates. Yet very little is known about their structural features or what makes these interactions transient. Paucity of such information has particularly affected our ability to engineer novel metabolic pathways, construct multi-scale mathematical models of cells, etc. We address this by obtaining a comprehensive map for 1225 interaction pairs in the essential 1-carbon metabolism pathway ofE. coli. Using both high-throughput experiments and computation, we uncover that metabolon proteins tend to use a conserved dedicated interface to interact with their partners. These results shed light on structural and energetic aspects of PPI in metabolons at near atomic level of resolution.
Mycorrhizal and endophytic fungi structure contrasting but interdependent assembly processes in forest below-ground symbiosis
Authors: Noguchi Mikihito , Toju Hirokazu 
Published: February 2024

AbstractInteractions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The nature of the symbiosis in root systems is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome structure, inter-root sharing/dispersal of symbionts, and fungus–fungus interactions within fine roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of mycorrhizal and endophytic fungal communities. Based on a framework of joint species distribution modeling, we here examined how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont–symbiont interactions. In our analysis targeting 1,615 root-tip samples collected in a cool-temperate forest dominated by ectomycorrhizal plants, statistical models including all the four ecological factors/processes best explained the fine-scale community structure of root-associated fungi. Meanwhile, among partial models including subsets of those ecological factors/processes, those including background soil microbiome structure and within-root fungus–fungus interactions showed the highest performance. When fine-root distributions of respective fugal species/taxa were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and stronger spatially-autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus–fungus interactions. A network statistical analysis further suggested that some endophytic fungi, such as those belonging to the ascomycete generaPhialocephalaandLeptodontidium, were involved in webs of positive and negative interactions with other root-associated fungi. These results suggest that basic assembly rules can differ between mycorrhizal and endophytic fungi, both of which are major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal functional guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant–fungal symbiosis.
High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales
Authors: Vasquez Kimberly S. , Wong Daniel P.G.H. , Pedro Miguel F. , Yu Feiqiao Brian , Jain Sunit , Meng Xiandong , Higginbottom Steven K. , DeFelice Brian C. , Neff Norma , Bhatt Ami , Tropini Carolina , Xavier Karina B. , Sonnenburg Justin L. , Good Benjamin H. , Huang Kerwyn Casey 
Published: February 2024

SummaryGut bacteria rapidly evolvein vivo, but their long-term success requires dispersal across hosts. Here, we quantify this interplay by tracking >50,000 genomically barcoded lineages of the prevalent commensalBacteroides thetaiotaomicron(Bt) among co-housed mice. We find that adaptive mutations rapidly spread between hosts, overcoming the natural colonization resistance of residentBtstrains. Daily transmission rates varied >10-fold across hosts, but shared selection pressures drove predictable engraftment of specific lineages over time. The addition of a 49-species community shifted the adaptive landscape relative to mono-colonizedBtwithout slowing the rate of evolution, and reduced transmission while still allowing specific mutants to engraft. Whole-genome sequencing uncovered diverse modes of adaptation involving complex carbohydrate metabolism. Complementaryin vitroevolution across 29 carbon sources revealed variable overlap within vivoselection pressures, potentially reflecting synergistic and antagonistic pleiotropies. These results show how high-resolution lineage tracking enables quantification of commensal evolution across ecological scales.
A Model of Ethanol Self-Administration in Head-Fixed Mice
Authors: Ward Amy L. , Winston Kion T. , Buchmaier Sophie A. , Clarke Rachel E. , Bell Marcus S. , Martino Michael R. , Vollmer Kelsey M. , Paniccia Jacqueline , Doncheck Elizabeth M. , Grant R. Ian , Otis James M. , Rinker Jennifer A. 
Published: February 2024

AbstractSignificant advances in neurotechnology, such as the emergence of 2-photon imaging, have enabled unparalleled access to the complex neural circuits that coordinate behavior in rodents. Integration of these techniques would be groundbreaking for the study of animal models of alcohol use disorder (AUD), which is rooted in longitudinal brain adaptations that could be functionally monitored and manipulated at the level of neural circuits from the onset of alcohol use through dependence. However, 2-photon and related methodologies require or are often facilitated by head-fixation, and a lack of head-fixed models have hindered their integration in the study of AUD. Here we present a head-fixed alcohol self-administration model, and find that head-fixed male and female mice will reliably press an active, but not inactive, lever for an oral alcohol reward. The number of alcohol rewards obtained reliably predicted blood alcohol concentrations, at physiologically relevant levels. Furthermore, we demonstrate that mice can extinguish alcohol self-administration when the alcohol reward is omitted, suggesting active lever pressing behavior was alcohol-directed. Following extinction, presentation of alcohol-related cues or a priming reminder of alcohol itself invigorated reinstatement of alcohol seeking, modeling relapse in a manner that mimics decades of work in freely-moving rodent studies. Overall, our head-fixed alcohol self-administration model allows integration of novel technologies that require or are greatly facilitated by head-fixation, improving our ability to study and understand the neural circuits adaptations and computations that underlie AUD.
A pre-vertebrate endodermal origin of calcitonin-producing neuroendocrine cells
Authors: Rees Jenaid M. , Kirk Katie , Gattoni Giacomo , Hockman Dorit , Ritter Dylan J. , Benito-Gutierrez Èlia , Knapik Ela W. , Crump J. Gage , Fabian Peter , Gillis J. Andrew 
Published: February 2024

SummaryVertebrate calcitonin-producing cells (C-cells) are neuroendocrine cells that secrete the small peptide hormone calcitonin in response to elevated blood calcium levels. C-cells are crucial for maintenance of calcium homeostasis, yet the embryonic and evolutionary origins of this cell type remain contentious. Whereas mouse C-cells reside within the thyroid gland and derive from pharyngeal endoderm, avian C-cells are located within ultimobranchial glands and were reported to derive from the neural crest. We use a comparative cell lineage tracing approach in a range of vertebrate model systems to resolve the ancestral embryonic origin of vertebrate C-cells. We find, contrary to previous studies, that chick C-cells derive from pharyngeal endoderm, with neural crest-derived cells instead contributing to connective tissue intimately associated with C-cells in the ultimobranchial gland. This endodermal origin of C-cells is conserved in a ray-finned bony fish (zebrafish) and a cartilaginous fish (the little skate,Leucoraja erinacea). Furthermore, we discover putative C-cell homologues within the endodermally-derived pharyngeal epithelium of the ascidianCiona intestinalisand the amphioxusBranchiostoma lanceolatum, two invertebrate chordates that lack neural crest cells. Our findings point to a conserved endodermal origin of C-cells across vertebrates and to a pre-vertebrate origin of this cell type along the chordate stem.
Social-ecological models with social hierarchy and spatial structure applied to small scale fisheries
Authors: Wulfing Sophie , White Easton R. 
Published: February 2024

1ABSTRACTSocio-ecological models combine ecological systems with human social dynamics in order to better understand human interactions with the environment. To model human behavior, replicator dynamics can be used to model how societal influence and financial costs can change opinions about resource extraction. Previous research on replicator dynamics has shown how evolving opinions on conservation can change how humans interact with their environment and therefore change population dynamics of the harvested species. However, social-ecological models often assume that human societies are homogeneous with no social structure. Building on previous work on social-ecological models, we develop a two-patch socio-ecological model with social hierarchy in order to study the interactions between spatial dynamics an social inequity. We found that fish movement between patches is a major driver of model dynamics, especially when the two patches exhibit different social equality and fishing practices. Further, we found that the societal influence between groups of harvesters was essential to ensuring stable fishery dynamics. Next, we developed a case-study of a co-managed fishery where one group fishes sustainably while another was over-harvests, resulting in a fishery collapse of both patches. We also found that because social influence only included number of fishers and not effective strategies, increased social pressure actually decreased the sustainability of the fishery. The findings of this study indicate the importance of including spatial components to socio-ecological models and highlights the importance of understanding species movements when making conservation decisions. Further, we demonstrate how incorporating fishing methods from outside sources can result in higher stability of the harvested population, indicating a need for diversified information when managing resources.
ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization
Authors: Shahneh Mohammad Reza Zare , Strobel Michael , Vitale Giovanni Andrea , Geibel Christian , Abiead Yasin El , Garg Neha , Aron Allegra T , Phelan Vanessa V , Petras Daniel , Wang Mingxun 
Published: February 2024

AbstractUntargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques such as MS/MS library search have enabled the re-identification of known compounds. Analog library search and molecular networking extend this identification to unknown compounds. While there have been advancements in metrics for the similarity of MS/MS spectra of structurally similar compounds, there is still a lack of automated methods to provide site specific information about structural modifications. Here we introduce ModiFinder that leverages the alignment of peaks in MS/MS spectra between structurally related known and unknown small molecules. Specifically, ModiFinder focuses on shifted MS/MS fragment peaks in the MS/MS alignment. These shifted peaks putatively represent substructures of the known molecule that contain the site of the modification. ModiFinder synthesizes these information together and scores the likelihood for each atom in the known molecule to be the modification site. We demonstrate in this manuscript how ModiFinder can effectively localize modifications which extends the capabilities of MS/MS analog searching and molecular networking to accelerate the discovery of novel compounds.
Retrotransposon-mediated variation of a chitin synthase gene confers insect resistance toBacillus thuringiensisVip3Aa toxin
Authors: Liu Zhenxing , Liao Chongyu , Zou Luming , Jin Minghui , Shan Yinxue , Quan Yudong , Yao Hui , Zhang Lei , Wang Peng , Liu Zhuangzhuang , Wang Na , Li Anjing , Liu Kaiyu , Heckel David G. , Wu Kongming , Xiao Yutao 
Published: February 2024

AbstractBacillus thuringiensis(Bt) crops expressing Vip3Aa are highly efficacious in controlling major lepidopteran pests and delaying evolution of pest resistance. Although practical resistance to Vip3Aa in the field has not been reported, to proactively manage the pest resistance, there is an urgent need to better understand the genetic basis of resistance to Vip3Aa. This is particularly important for the fall armyworm (Spodoptera frugiperda), one of the most destructive pests around the world, which has evolved practical resistance toBtcrystal (Cry) toxins. Here, a highly Vip3Aa-resistant (resistance ratio: 5,562-fold) strain ofS. frugiperdawas selected in the laboratory. Results from bulked segregant analysis, fine-scale mapping, and genetic linkage analysis indicate that a mutation in the midgut-specific chitin synthase gene,SfCHS2, is strongly associated with high-level resistance to Vip3Aa. The resistance is ascribed to the transcriptional variation caused by retrotransposon insertion. The same variation ofSfCHS2was also detected in a field population. Importantly, knockout ofSfCHS2via CRISPR/Cas9 in susceptibleS. frugiperdaconfers its complete resistance (>10,000-fold) to Vip3Aa. Also, we demonstrate that knockout ofCHS2can result in complete resistance to Vip3Aa in additional lepidopteran species, suggesting a general role of this gene in Vip3Aa resistance among lepidopteran pests. These results reported here would contribute to monitor and management of pest resistance to Vip3Aa.
Mimicking Human EED Variants in Drosophila: A Promising Strategy to Analyse Human EED Variant Function
Authors: Cyrus Sharri S. , Giró Sònia Medina , Lian Tianshun , Allan Douglas W. , Gibson William T. 
Published: February 2024

AbstractThe Polycomb Repressive Complex 2 is an epigenetic reader/writer that methylates histone H3K27. Rare germline partial loss of function (pLoF) variants in core members of the complex (EZH2, EED, SUZ12) cause overgrowth and intellectual disability syndromes, whereas somatic variants are implicated in cancer. However, up to 1% of the general population will have a rare variant in one of these genes, most of which would be classified as variants of uncertain significance (VoUS). Towards screening these VoUS for partial LoF alleles that may contribute to disease, here we report functional assays inDrosophilato interrogateEEDmissense variants. We mimicked the amino acid change(s) ofEEDvariants into itsDrosophilaortholog,esc, and tested their function. Known likely benign variants functioned wildtype and known pathogenic variants were LoF. We further demonstrate the utility of this calibrated assay as a scalable approach to assist clinical interpretation of humanEEDVoUS.