bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrophysiological Markers of Memory Consolidation in the Human Brain when Memories are Reactivated during Sleep
Authors: Creery Jessica D. , Brang David J. , Arndt Jason D. , Bassard Adrianna , Towle Vernon L. , Tao James X. , Wu Shasha , Rose Sandra , Warnke Peter C. , Issa Naoum , Paller Ken A. 
Published: June 2022

AbstractHuman accomplishments depend on learning, and effective learning depends on consolidation. Consolidation is the process whereby new memories are gradually stored in an enduring way in the brain so that they can be available when needed. For factual or event knowledge, consolidation is thought to progress during sleep as well as during waking states, and to be mediated by interactions between hippocampal and neocortical networks. However, consolidation is difficult to observe directly, but rather is inferred through behavioral observations. Here, we investigated overnight memory change by measuring electrical activity in and near the hippocampus. Electroencephalographic (EEG) recordings were made in five patients from electrodes implanted to determine whether a surgical treatment could relieve their seizure disorders. One night, while each patient slept in a hospital monitoring room, we recorded electrophysiological responses to 10-20 specific sounds that were presented very quietly, to avoid arousal. Half of the sounds had been associated with objects and their precise spatial locations that patients learned before sleep. After sleep, we found systematic improvements in spatial recall, replicating prior results. We assume that when the sounds were presented during sleep, they reactivated and strengthened corresponding spatial memories. Notably, the sounds also elicited oscillatory intracranial EEG activity, including increases in theta, sigma, and gamma EEG bands. Gamma responses, in particular, were consistently associated with the degree of improvement in spatial memory exhibited after sleep. We thus conclude that this electrophysiological activity in the hippocampus and adjacent medial temporal cortex reflects sleep-based enhancement of memory storage.Significance StatementSleep contributes to memory consolidation, we presume, because memories are replayed during sleep. Understanding this aspect of consolidation can help with optimizing normal learning in many contexts, and with treating memory disorders and other diseases. Here, we systematically manipulated sleep-based processing using targeted memory reactivation; brief sounds coupled with pre-sleep learning were quietly presented again during sleep, producing (a) recall improvements for specific spatial memories associated with those sounds, and (b) physiological responses in the sleep EEG. Neural activity in the hippocampus and adjacent medial temporal cortex was thus found in association with memory consolidation during sleep. These findings advance understanding of consolidation by linking beneficial memory changes during sleep to both memory reactivation and specific patterns of brain activity.
Macroscale Adipose Tissue from Cellular Aggregates: A Simplified Method of Mass Producing Cell-Cultured Fat for Food Applications
Authors: Yuen John SK , Saad Michael K , Xiang Ning , Barrick Brigid M , DiCindio Hailey , Li Chunmei , Zhang Sabrina W , Rittenberg Miriam , Lew Emily T , Leung Glenn , Pietropinto Jaymie A , Kaplan David L 
Published: June 2022

AbstractWe present a method of producing bulk cell-cultured fat tissue for food applications. Mass transport limitations (nutrients, oxygen, waste diffusion) of macroscale 3D tissue culture are circumvented by initially culturing murine or porcine adipocytes in 2D, after which bulk fat is produced by mechanically harvesting and aggregating the lipid-filled adipocytes into 3D fats using alginate or transglutaminase binders. The 3D fats were visually similar to fat tissue harvested from animals, with matching textures based on uniaxial compression tests. The mechanical properties of cultured fat tissues were based on binder choice and concentration, and changes in the fatty acid compositions of cellular triacylglyceride and phospholipids were observed after lipid supplementation (soybean oil) during in vitro culture. This approach of aggregating individual adipocytes into a bulk 3D tissue provides a scalable and versatile strategy to produce cultured fat tissue for food-related applications, thereby addressing a key obstacle in cultivated meat production.Graphical Abstract
Quantifying chemodiversity considering biochemical and structural properties of compounds with the R packagechemodiv
Authors: Petrén Hampus , Köllner Tobias G. , Junker Robert R. 
Published: June 2022

SummaryPlants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds.Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds’ function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures.We introduce the R packagechemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and – most importantly – structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets.By providing the R packagechemodivfor quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.
AMPK deficiency in smooth muscles causes persistent pulmonary hypertension after birth and premature death
Authors: Moral-Sanz Javier , Lewis Sophronia A. , MacMillan Sandy , Meloni Marco , McClafferty Heather , Viollet Benoit , Foretz Marc , del-Pozo Jorge , Evans A. Mark 
Published: June 2022

AbstractWe address a paradox, that AMPK may facilitate hypoxic pulmonary vasoconstriction and its deficiency precipitate pulmonary hypertension. Here we show that AMPK-α1/α2 deficiency in smooth muscles promotes persistent pulmonary hypertension of the newborn. Accordingly, dual AMPK-α1/α2 deletion in smooth muscles causes premature death of mice after birth, associated with increased muscularization and remodeling throughout the pulmonary arterial tree, reduced alveolar numbers and alveolar membrane thickening, but with no edema. Spectral Doppler ultrasound indicates pulmonary hypertension and attenuated hypoxic pulmonary vasoconstriction. Age-dependent right ventricular pressure elevation, dilation and reduced cardiac output was also evident. KV1.5 potassium currents of pulmonary arterial myocytes are markedly smaller under normoxia, which is known to facilitate pulmonary hypertension. Mitochondrial fragmentation and reactive oxygen species accumulation is also evident. Importantly, there is no evidence of systemic vasculopathy or hypertension in these mice. Moreover, hypoxic pulmonary vasoconstriction is attenuated by AMPK-α1 or AMPK-α2 deletion without triggering pulmonary hypertension.
Overall patterns of eye-specific retino-geniculo-cortical projections to layers III, IV and VI in primary visual cortex of the prosimian galago, and correlation with cytochrome oxidase blobs
Authors: Olavarria Jaime F. , Qi Huixin , Takahata Toru , Kaas Jon H. 
Published: June 2022

AbstractStudies in galago have not provided a comprehensive description of the organization of eye specific retino-geniculate-cortical projections to the recipient layers in V1. Here we demonstrate the overall patterns of ocular dominance domains in layers III, IV and VI revealed after injecting the transneuronal tracer wheat germ agglutinin conjugated to horseradish peroxidase (WGA- HRP) into one eye. We also correlate these patterns with the array of cytochrome oxidase (CO) blobs in tangential sections through the unfolded and flattened cortex. In layer IV, we observed for the first time that eye-specific domains form an interconnected pattern of bands 200-250 um wide arranged such that they do not show orientation bias and do not meet the V1 border at right angles, as is the case in macaques. We also observed distinct patterns of ocular dominance patches in layer III and layer VI. The patches in layer III, likely corresponding to patches of K LGN input described previously, align with layer IV ocular dominance columns (ODCs) of the same eye dominance. Moreover, the layer III patches overlap partially with virtually all CO blobs in both hemispheres, implying that CO blobs receive K LGN input from both eyes. Finally, we found that CO blobs straddle the border between neighboring layer IV ODCs. These results, together with studies showing that a high percentage of cells in CO blobs are monocular, suggest that CO blobs consist of ipsilateral and contralateral subregions that are in register with underlying layer IV ocular dominance columns of the same eye dominance. In macaques and humans, CO blobs are centered on ODCs in layer IV. Our finding that CO blobs in galago straddle the border of neighboring layer IV ODCs suggests that this may represent an alternative way by which visual information is processed by eye specific modular architecture in mammalian V1.
Long wavelength light reduces the negative consequences of dim light at night in the Cntnap2 mouse model of autism
Authors: Wang Huei Bin , Zhou David , Luk Shu Hon Christopher , Cha Hye In , Mac Amanda , Chae Rim , Matynia Anna , Harrison Ben , Afshari Sina , Block Gene D. , Ghiani Cristina A. , Colwell Christopher S. 
Published: June 2022

AbstractMany patients with autism spectrum disorders (ASD) show disturbances in their sleep/wake cycles, and may be particularly vulnerable to the impact of circadian disruptors. We have previously shown that exposure to dim light at night (DLaN) in contactin associated protein-like 2 knock out (Cntnap2 KO) mice disrupts diurnal rhythms, increases repetitive behaviors while reducing social interactions. These negative effects of DLaN may be mediated by intrinsically photosensitive retinal ganglion cells (ipRGCs) expressing the photopigment melanopsin, which is maximally sensitive to blue light (480nm). In this study, we used a light-emitting diode (LED) array that enabled us to shift the spectral properties of the DLaN while keeping the intensity at 10 lx. First, using wild-type (WT) mice, we confirmed that the short-wavelength enriched lighting produced strong acute suppression of locomotor activity (masking), robust light-induced phase shifts, and c-Fos expression in the suprachiasmatic nucleus, while the long-wavelength enriched lighting evoked much weaker responses. Furthermore, exposure of WT mice to the short-wavelength light at night reduced the amplitude of locomotor activity rhythms and impaired social interactions. Mice lacking the melanopsin expressing ipRGCs (Opn4DTA mice) were resistant to these negative effects of DLaN. Importantly, the shift of the DLaN stimulus to longer wavelengths ameliorated the negative impact on the activity rhythms and autistic behaviors (i.e. reciprocal social interactions, repetitive grooming) of the Cntnap2 KO model. The short-, but not the long-wavelength enriched, DLaN triggered cFos expression in the peri-habenula region as well as in the basolateral amygdala (BLA). Finally, DLaN-driven c-Fos induction in BLA glutamatergic neurons was about 3-fold higher in the Cntnap2 KO mice, suggesting that these cells may be particularly vulnerable to the effects of photic disruption. Broadly, our findings suggest that the spectral properties of light at night should be considered in the management of ASD and other neurodevelopmental disorders.
GeneToList: A web application to assist with gene identifiers for the non-bioinformatics-savvy scientist
Authors: Breidenbach Joshua D. , Begue E. Francis , Kennedy David J. , Haller Steven T. 
Published: June 2022

AbstractThe increasing incorporation of omics technology into clinical and translational medicine presents challenges to end users of the large and complex datasets that are generated by these methods. A particular challenge in genomics is that the nomenclature for genes is not uniform between large genomic databases or between commonly used genetic analysis tools. Furthermore, outdated genomic nomenclature can still be found amongst scientific communications including peer-reviewed manuscripts. Therefore, a web application (GeneToList) was developed to assist is gene ID conversion and alias matching, with a specific focus on achieving a user-friendly interface for the non-bioinformatics-savvy scientist.Availability and implementationGeneToList is available at https://www.genetolist.com/. The tool is a web application that is compatible with many standard browsers.ContactJoshua.Breidenbach@UToledo.edu or support@genetolist.com
Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase
Authors: Amstrup Søren K. , Sofos Nicholas , Karlsen Jesper L. , Skjerning Ragnhild B. , Boesen Thomas , Enghild Jan J. , Hove-Jensen Bjarne , Brodersen Ditlev E. 
Published: June 2022

ABSTRACTPhosphorus is an essential macronutrient for all microorganisms and can be extracted from the environment by several metabolic pathways. In Escherichia coli, the 14-cistron phn operon encoding the carbon-phosphorus (C-P) lyase enzymatic machinery allows for extraction of phosphorus from a wide range of phosphonates characterised by the highly stable C-P bond.1, 2 As part of a complex, multi-step pathway, the PhnJ subunit was proposed to cleave the C-P bond via a radical reaction, however, the details of the mechanism were not immediately compatible with the structure of the 220 kDa PhnGHIJ C-P lyase core complex, leaving a significant gap in our understanding of phosphonate breakdown in bacteria.3, 4 Here we show using single-particle cryogenic-electron microscopy that PhnJ mediates binding of a unique double dimer of ATP-binding cassette (ABC) proteins, PhnK and PhnL to the core complex. ATP hydrolysis by PhnK induces drastic structural remodelling leading to opening of the core and reconfiguration of a metal-binding site located at the interface between the PhnI and PhnJ subunits. Our results offer new insights into the mechanism underlying C-P lyase and uncover a hitherto unknown configuration of ABCs that have wide-ranging implications for our understanding of the role of this module in biological systems.
Dual IgA/IgG family autoantibodies from individuals at-risk for rheumatoid arthritis identify an arthritogenic strain ofSubdoligranulum
Authors: Chriswell Meagan , Lefferts Adam R. , Clay Michael , Hsu Alex , Seifert Jennifer , Feser Marie L. , Rims Cliff , Bloom Michelle , Bemis Elizabeth A. , Demoruelle M. Kristen , Deane Kevin D. , James Eddie A. , Buckner Jane H. , Robinson William H. , Holers V. Michael , Kuhn Kristine A. 
Published: June 2022

AbstractThe mucosal origins hypothesis of rheumatoid arthritis (RA) proposes a central role for mucosal immune responses in the initiation and/or perpetuation of the systemic autoimmunity that occurs with disease. However, the connection between the mucosa and systemic autoimmunity in RA remains unclear. Using dual IgA/IgG family plasmablast-derived monoclonal autoantibodies obtained from peripheral blood of individuals at-risk for RA, we identified cross-reactivity between RA-relevant autoantigens and bacterial taxa in the closely related familiesLachnospiraceaeandRuminococcaceae. After generating bacterial isolates withinLachnospiraceae/RuminococcaceaegenusSubdoligranulumfrom the feces of an individual, we confirmed monoclonal antibody binding as well as MHC class II dependent CD4+ T cell activation in RA cases compared to controls. Additionally, whenSubdoligranulumisolate 7 but not isolate 1 colonized germ-free mice, it stimulated Th17 cell expansion, serum RA-relevant IgG autoantibodies, and joint swelling reminiscent of early RA with histopathology characterized by antibody deposition and complement activation. Systemic immune responses were likely due to the generation of colon isolated lymphoid follicles (ILFs) driving increased fecal and serum IgA by isolate 7, as B and T cell depletion not only halted intestinal immune responses but also eliminated detectable clinical disease. In aggregate, these findings demonstrate one mucosal mechanism in RA through which an intestinal strain of bacteria can drive systemic autoantibody generation and joint-centered antibody deposition and immune activation.One-sentence summarySubdoligranulum spp.targeted by rheumatoid arthritis (RA)-relevant autoantibodies activate T cells in individuals with RA, and in mice stimulate autoantibodies and joint swelling associated with antibody deposition and complement activation.
Beyond winglets: evolutionary scaling of flight-related morphology in stick insects (Phasmatodea)
Authors: Zeng Yu , Park Sehoon , Gonzales Camille , Yom Stephanie , Rahim Faszly , Dudley Robert 
Published: June 2022

AbstractThe first winged insects evolved from a wingless ancestor, but details of the transition to a fully-winged morphology remain unclear. Studying extant pterygotes with partial wings, such as the stick insects (Order Phasmatodea), may help us to understand such a transition. Here, we address how a series of flight-related morphological parameters may correlate with flight evolution by studying different phasmids representing a volancy continuum ranging from miniaturized to full-sized wings. Variation in phasmid wing shape, venation, wing mass and the mass of flight muscle can be described by specific scaling laws referenced to wing length and wing loading. Also, the mass distribution of the body-leg system is conserved in spite of a wide range of variation in body shape. With reduced wing size and increased wing loading, the longitudinal position of the wing-bearing thoracic segments is shifted closer to the insects’ center of body mass. These results demonstrate complex reconfiguration of the flight system during wing morphological transitions in phasmids, with various anatomical features potentially correlated with reduced flight performance attained with partial wings. Although these data represent phasmid-specific features of the flight apparatus and body plan, the associated scaling relationships can provide insight into functionality of intermediate conditions between wingless and fully-winged insects more generally.
Using Interpretable Machine Learning to Massively Increase the Number of Antibody-Virus Interactions Across Studies
Authors: Einav Tal , Ma Rong 
Published: June 2022

AbstractA central challenge in every field of biology is to use existing measurements to predict the outcomes of future experiments. In this work, we consider the wealth of antibody inhibition data against variants of the influenza virus. Due to this virus’s genetic diversity and evolvability, the variants examined in one study will often have little-to-no overlap with other studies, making it difficult to discern common patterns or unify datasets for further analysis. To that end, we develop a computational framework that predicts how an antibody or serum would inhibit any variant fromany other study. We use this framework to greatly expand seven influenza datasets utilizing hemagglutination inhibition, validating our method upon 200,000 existing measurements and predicting 2,000,000 new values ± uncertainties. With these new values, we quantify the transferability between seven vaccination and infection studies in humans and ferrets, show that the serum potency is negatively correlated with breadth, and present a tool for pandemic preparedness. This data-driven approach does not require any information beyond each virus’s name and measurements, and even datasets with as few as 5 viruses can be expanded, making this approach widely applicable. Future influenza studies using hemagglutination inhibition can directly utilize our curated datasets to predict newly measured antibody responses against ≈80 H3N2 influenza viruses from 1968-2011, whereas immunological studies utilizing other viruses or a different assay only need a single partially-overlapping dataset to extend their work. In essence, this approach enables a shift in perspective when analyzing data from “what you see is what you get” into “what anyone sees is what everyone gets.”
From pseudotime to true dynamics: reconstructing a real-time axis for T cells differentiation
Authors: Gavish Avishai , Chain Benny , Salame Tomer M , Antebi Yaron E , Katz Shir , Reich-Zeliger Shlomit , Friedman Nir 
Published: June 2022

AbstractNumerous methods have recently emerged for ordering single cells along developmental trajectories. However, accurate depiction of developmental dynamics can only be achieved after rescaling the trajectory according to the relative time spent at each developmental point. We formulate a model which estimates local cell densities and fluxes, and incorporates cell division and apoptosis rates, to infer the real time dimension of the developmental trajectory. We validate the model using mathematical simulations, and apply it on experimental high dimensional cytometry data obtained from the mouse thymus to construct the true time-profile of the thymocyte developmental process. Our method can easily be implemented in any of the existing tools for trajectory inference.
DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy
Authors: Sonet Gontran , Smitz Nathalie , Vangestel Carl , Samyn Yves 
Published: June 2022

AbstractEchinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5’ end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (>5% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.