bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stereochemistry Determines Immune Cellular Responses to Polylactide Implants
Authors: Maduka Chima V. , Alhaj Mohammed , Ural Evran , Kuhnert Maxwell M. , Habeeb Oluwatosin M. , Schilmiller Anthony L. , Hankenson Kurt D. , Goodman Stuart B. , Narayan Ramani , Contag Christopher H. 
Published: October 2022

ABSTRACTRepeating L- and D-chiral configurations determine polylactide (PLA) stereochemistry which affects its thermal and physicochemical properties, including degradation profiles. Clinically, degradation of implanted PLA biomaterials promotes prolonged inflammation and excessive fibrosis, but the role of PLA stereochemistry is unclear. Additionally, although PLA of varied stereochemistries cause differential immune responses in-vivo, this observation has yet to be effectively modeled in-vitro. A bioenergetic model was applied to study immune cellular responses to PLA containing > 99% L-lactide (PLLA), > 99% D-lactide (PDLA) and a 50/50 melt-blend of PLLA and PDLA (stereocomplex PLA). Stereocomplex PLA breakdown products increased IL-1β, TNF-α and IL-6 protein levels but not MCP-1. Expression of these proinflammatory cytokines is mechanistically driven by increases in glycolysis in primary macrophages. In contrast, PLLA and PDLA degradation products selectively increase MCP-1 protein expression. Whereas both oxidative phosphorylation and glycolysis are increased with PDLA, only oxidative phosphorylation is increased with PLLA. For each biomaterial, glycolytic inhibition reduces proinflammatory cytokines and markedly increases anti-inflammatory (IL-10) protein levels; differential metabolic changes in fibroblasts were observed. These findings provide mechanistic explanations for the diverse immune responses to PLA of different stereochemistries, and underscore the pivotal role of immunometabolism on the biocompatibility of biomaterials applied in medicine.
Identifying Neuropsychiatric Disorder Subtypes and Subtype-dependent Variation in Diagnostic Deep Learning Classifier Performance
Authors: Ellis Charles A. , Miller Robyn L. , Calhoun Vince D. 
Published: October 2022

ABSTRACTClinicians and developers of deep learning-based neuroimaging clinical decision support systems (CDSS) need to know whether those systems will perform well for specific individuals. However, relatively few methods provide this capability. Identifying neuropsychiatric disorder subtypes for which CDSS may have varying performance could offer a solution. Dynamic functional network connectivity (dFNC) is often used to study disorders and develop neuroimaging classifiers. Unfortunately, few studies have identified neurological disorder subtypes using dFNC. In this study, we present a novel approach with which we identify 4 states of dFNC activity and 4 schizophrenia subtypes based on their time spent in each state. We also show how the performance of an explainable diagnostic deep learning classifier is subtype-dependent. We lastly examine how the dFNC features used by the classifier vary across subtypes. Our study provides a novel approach for subtyping disorders that (1) has implications for future scientific studies and (2) could lead to more reliable CDSS.
Effects of chitin and chitosan on root growth, biochemical defense response and exudate proteome ofCannabis sativa
Authors: Suwanchaikasem Pipob , Nie Shuai , Idnurm Alexander , Selby-Pham Jamie , Walker Robert , Boughton Berin A. 
Published: October 2022

AbstractFungal pathogens pose a major threat toCannabis sativaproduction, requiring safe and effective management procedures to control disease. Chitin and chitosan are natural molecules that elicit plant defense responses. Investigation of their effects onC. sativawill advance understanding of plant responses towards elicitors and provide a potential pathway to enhance plant resistance against diseases. Plants were grown in thein vitroRoot-TRAPR system and treated with colloidal chitin and chitosan. Plant morphology was monitored, then plant tissues and exudates were collected for enzymatic activity assays, phytohormone quantification, qPCR analysis and proteomics profiling. Chitosan treatments showed increased total chitinase activity and expression of pathogenesis-related (PR) genes by 3-5 times in the root tissues. In the exudates, total peroxidase and chitinase activities and levels of defense proteins such as PR protein 1 and endochitinase 2 were increased. Shoot development was unaffected, but root development was inhibited after chitosan exposure. No significant effects on plant defense were observed upon chitin treatment. These results indicate that colloidal chitosan significantly promoted production and secretion of plant defense proteins inC. sativaroot system and could be used as a potential elicitor, particularly in hydroponic scenarios to manage crop diseases.HighlightChitosan induces defense protein productions and secretions in the root tissues and exudates ofC. sativa, offering a potential pathway to enhance plant resistance against fungal attack.
An Inducible T7 Polymerase System for High-Level Protein Expression in Diverse Gram-Negative Bacteria
Authors: Greenwich Jennifer L. , Alakavuklar Melene A. , Fuqua Clay 
Published: October 2022

ABSTRACTA broad host range (BHR) inducible T7 RNA Polymerase system was developed, enabling induction with IPTG, similar to theEscherichia colistrain BL21(DE3), but now applicable in a wide range of bacteria. This allows for high protein yields and purification from diverse gram-negative bacteria including the native host.
Acellular Cartilage-Bone Allografts Restore Structure, Mechanics, and Surface Properties In Vivo, but Limit Recellularization and Integrative Repair
Authors: Barthold Jeanne E. , Cai Luyao , McCreery Kaitlin P. , Fischenich Kristine , Eckstein Kevin , Ferguson Virginia , Emery Nancy , Breur Gert , Neu Corey P. 
Published: October 2022

ABSTRACTThe repair of articular cartilage after damage is challenging, and clinical interventions to promote regeneration remain elusive. The most effective treatment for cartilage defects utilizes viable osteochondral allografts from young donors, but unfortunately suffers from severe source limitations and short storage time. Decellularized tissue offers the potential to utilize native tissue structure and composition while also overcoming source limitations, but the long-term efficacy of acellular allografts is unknown. Here, we show that acellular osteochondral allografts improve functional and integrative cartilage repair in defect regions after 6 months in a preclinical (sheep) animal model. Functional measures of intratissue strain and structure assessed by MRI demonstrate similar biomechanical performance between implants and native cartilage. Compared to native tissue, the structure, composition, and tribology of acellular allografts conserve surface roughness and lubrication, native cartilage material properties under compression and relaxation, and compositional ratios of collagen:glycosaminoglycan and collagen:phosphate. However, while high cellularity was observed in the integration zones between native cartilage and acellular allografts, recellularization throughout the chondral implant was largely lacking, potentially limiting long-term cellular maintenance in the graft and repair success. Our results advance a suite of joint-to-cellular functional assays, demonstrate the biomechanical efficacy of acellular allografts for at least six monthsin vivo, and suggest that long-term implant success may suffer from a lack of cell migration into the dense decellularized chondral tissue.
Phase separation as higher-order catalyst
Authors: Huang Kai , Quan Xuebo , Qin Shiyi 
Published: October 2022

AbstractThe long-distance communication between multiple cis-regulatory elements (CREs), the self-limiting size and lifetime of regulatory condensates, are two puzzling phenomena in biology. To reconcile these puzzles, we introduce the concept of higher-order catalysis into chromatin-mediated reactions. Essentially, multi-way contact between the CREs defines a transition state that is required for the downstream cascade of chemical reactions. The entropic penalty of chromatin reorganization sets a high activation barrier to enter this transition state. Phase separation of trans-acting agents induced by the CREs reduces this barrier and stabilizes the transition state via forming a regulatory condensate. The downstream reaction then pays back energy to dissolve the condensate and resets the agents to a metastable single-phase state. Accelerating the reactions without consuming agents or changing their state, the cycled phase transitions construct a higher-order catalyst or super-enzyme that is beyond the form of a single molecule. We discuss how chromatin employs such super-enzymes to catalyze higher-order reactions mediated by itself.
miR-223 Plays A Critical Role in Obesogen-Enhanced Adipogenesis in Mesenchymal Stem Cells and in Transgenerational Obesity
Authors: Chang Richard C. , Joloya Erika M. , Li Zhuorui , Shoucri Bassem M. , Shioda Toshi , Blumberg Bruce 
Published: October 2022

AbstractExposure of pregnant F0 mouse dams to the obesogen tributyltin (TBT) predisposes unexposed male descendants to obesity and diverts mesenchymal stem cells (MSCs) toward the adipocytic lineage. TBT also promotes adipogenic commitment and differentiation of MSCs, in vitro. We sought to identify TBT-induced factors predisposing MSCs toward the adipocytic fate. We exposed mouse MSCs to TBT, the PPARγ-selective agonist rosiglitazone or the RXR-selective agonist LG-100268 and determined their transcriptomal profiles to determine candidate microRNAs (miR) regulating adipogenic commitment and differentiation. Of the top 10 candidate microRNAs predicted by Ingenuity Pathway Analysis, miR-21, miR-33 and miR-223 were expressed in a manner consistent with an ability to differentially regulate target genes during adipogenesis. After 24 hours exposure to 50 nM TBT, miR-223 levels in MSCs were increased and expression of its target genes ZEB1, NFIB, and FOXP1 was decreased. Both ROSI and TBT increased miR-223 levels, and this induction was inhibited by the PPARγ antagonist T0070907 but not by the RXR antagonists HX531 or UVI3003, placing miR-223 downstream of PPARγ. Chromatin immunoprecipitation confirmed TBT-induced binding of PPARγ to regulatory elements in the miR-223 promoter. miR-223 levels were elevated in white adipose tissue of F2 and F3 male descendants of pregnant F0 mouse dams exposed to 50 nM TBT throughout gestation. miR-223 levels were further induced in males fed with an increased fat diet. We infer that TBT induced miR-223 expression and increased adipogenesis in MSCs through the PPARγ pathway and that transgenerationally increased expression of miR-223 plays an important role in the development of obesity caused by TBT exposure.
Using the AKAR3-EV biosensor to assess Sch9- & PKA-signalling in budding yeast
Authors: Botman Dennis , Kanagasabapathi Sineka , Teusink Bas 
Published: October 2022

AbstractBudding yeast uses the well-conserved TORC1-Sch9 and cAMP-PKA signalling pathways to regulate adaptations to changing nutrient environments. Dynamic and single-cell measurements of the activity of these two cascades will improve our understanding of cellular adaptation of yeast. Here, we employed the AKAR3-EV biosensor developed for mammalian cells to measure the cellular phosphorylation status determined by Sch9 and PKA activity in budding yeast. Using various mutant strains and inhibitors, we show that AKAR3-EV robustly measures the Sch9- and PKA-dependent phosphorylation status in intact yeast cells. At the single-cell level, we found that the phosphorylation responses are homogenous for glucose, sucrose and fructose, but highly heterogeneous for mannose. The Sch9 and PKA pathways have a relatively high affinity for glucose (K0.5of 0.24 mM) under glucose derepressed conditions. Lastly, steady-state FRET levels of AKAR3-EV seem to be independent of growth rates, suggesting that the Sch9- and PKA-dependent phosphorylation activity are transient responses to nutrient transitions. We believe that the AKAR3-EV sensor is an excellent addition to the biosensor arsenal for illuminating cellular adaptation in single yeast cells.
A whole blood intracellular cytokine assay optimised for field site studies demonstrates polyfunctionality of CD4+ T cells in acute scrub typhus
Authors: Inthawong Manutsanun , Pinthong Nattapon , Thaiprakhong Areerat , Wangrangsimakul Tri , Sunyakumthorn Piyanate , Hill Jennifer , Sonthayanon Piengchan , Paris Daniel H. , Dunachie Susanna , Kronsteiner Barbara 
Published: October 2022

AbstractBackgroundAssessment of cellular immune responses by combining intracellular cytokine staining and immunophenotyping using flow cytometry enables the simultaneous measurement of T cell phenotype and effector function in response to pathogens and vaccines. The use of whole blood samples rather than peripheral blood mononuclear cells avoids both the need for immediate processing and loss of functional antigen presenting cells due to processing and cryopreservation. Using whole blood provides the possibility to stimulate peripheral T cellsin situ, and is more suitable for studies where sample volume is limited, such as those involving children, the elderly and critically ill patients. The aim of this study was to provide a robust tool for the assessment of antigen-specific T cell responses in a field site setting with limited resources.Methodology/Principle FindingsWe optimised a flow cytometry-based whole blood intracellular cytokine assay (WBA) with respect to duration of antigen stimulation and intracellular protein retention time. We demonstrate the ability of the WBA to capture polyfunctional T cell responses in the context of acute scrub typhus infection, by measuring IFN-γ, TNF and IL-2 in CD4+ and CD8+ T cells in response to the causative agentO. tsutsugamushi(OT). Using an optimised OT antigen preparation, we demonstrate the presence of polyfunctional antigen-specific memory CD4+ T cells in the blood of scrub typhus patients.Conclusions/SignificanceIn conclusion, this flow cytometry-based WBA is well-suited for use at field study sites, and enables the assessment of polyfunctional T cell responses to infectious agents and vaccines through delineation of antigen-specific cytokine secretion at the single cell level.Author summaryScrub typhus is an acute febrile illness caused by the bite of infected chigger mites transmittingO. tsutsugamushi, agramnegative obligate intracellular bacteria in the familyRickettsiaceae. The disease progression and clinical manifestations are closely associated with host immune responses. T cell responses are in strong relation with immune protection against scrub typhus. As there is limited knowledge on specific T cell roles against scrub typhus, we optimized a flow-cytometer based protocol to assessO. tsutsugumushi-specific T cell responses in whole blood samples, which is suitable for studies in limited resource settings. This method requires low blood volumes, but enables multiparametric immunophenotyping assessments. The optimized WBA protocol could be a useful tool for comprehensive immunopathological studies in scrub typhus, and other infectious diseases as well as vaccine studies in areas with limited availability of specialized equipment, while reliably capturing the complexity of the immune response.
The Rapid-Tome, a 3D-Printed Microtome, and an Updated Hand-Sectioning Method for High-Quality Plant Sectioning
Authors: Thomas David J. , Rainbow Jordan , Bartley Laura E. 
Published: October 2022

AbstractBackgroundMicroscopic analysis of plant anatomy is a common procedure in biology to study structure and function that requires high-quality sections for accurate measurements. Hand sectioning of specimens is typically limited to moderately soft tissue while harder samples prohibit sectioning by hand and/or result in inconsistent thicknesses.ResultsHere we present both a clearly described hand-sectioning method and a novel microtome design that together provide the means to section a variety of plant sample types. The described hand-sectioning method for herbaceous stems works well for softer subjects but is less suitable for samples with secondary growth (e.g., wood production). Instead, the “Rapid-Tome” is a novel tool for sectioning both soft and tougher high-aspect-ratio samples, such as stems and roots, with excellent sample control. The Rapid-Tome can be 3D-printed in approximately 13 hours on a mid-quality printer common at university maker spaces. After printing and trimming, Rapid-Tome assembly takes a few minutes with five metal parts common at hardware stores. Users sectioned a variety of plant samples including the hollow internodes of switchgrass (Panicum virgatum), fibrous switchgrass roots containing aerenchyma, and woody branches of eastern red cedar (Juniper virginiana) and American sycamore (Platanus occidentalis). A comparative analyses with Rapid-Tome-produced sections readily revealed a significant difference in seasonal growth of sycamore xylem vessel area in spring (49%) vs. summer (23%). Additionally, high school students with no prior experience produced sections with the Rapid-Tome adequate for comparative analyses of various plant samples in less than an hour.ConclusionsThe described hand-sectioning method is suitable for softer tissues, including hollow-stemmed grasses and similar samples. In addition, the Rapid-Tome provides capacity to safely produce high-quality sections of tougher plant materials at a fraction of the cost of traditional microtomes combined with excellent sample control. The Rapid-Tome features rapid sectioning, sample advancement, blade changes, and sample changes; is highly portable and can be used easily with minimal training making production of thin sections accessible for classroom and outreach use, in addition to research.
BrainPy: a flexible, integrative, efficient, and extensible framework towards general-purpose brain dynamics programming
Authors: Wang Chaoming , Chen Xiaoyu , Zhang Tianqiu , Wu Si 
Published: October 2022

AbstractThe neural mechanisms underlying brain functions are extremely complicated. Brain dynamics modeling is an indispensable tool for elucidating these mechanisms by modeling the dynamics of the neural circuits that execute brain functions. To ease and facilitate brain dynamics modeling, a general-purpose programming framework is needed to enable users to freely define neural models across multiple scales; efficiently simulate, train, and analyze model dynamics; and conveniently extend new modeling approaches. By utilizing the advanced just-in-time (JIT) compilation, we developed BrainPy. BrainPy provides a rich infrastructure tailored for brain dynamics programming, which supports an integrated platform for brain dynamics model building, simulation, training, and analysis. Models in BrainPy can be JIT compiled into binary instructions for multiple devices (including CPU, GPU, and TPU) to achieve a high running performance comparable to native C or CUDA. Moreover, BrainPy features an extensible architecture allowing easy expansion of new infrastructure, utilities, and machine learning approaches.
SMbiot: A Shared Latent Model for Microbiomes and their Hosts
Authors: Krishnamurthy Madan , Herron Lukas , Susanti Dwi , Volland-Munson Alyssa , Plata Germán , Dixit Purushottam 
Published: October 2022

AbstractThe collective nature of the variation in host associated microbial communities suggest that they exhibit low dimensional characteristics. To identify these lower dimensional descriptors, we propose SMbiot (pronounced SIM BY OT): aShared LatentModel for Microbiomes and their hosts. In SMbiot, latent variables embed host-specific microbial communities in a lower dimensional space and the corresponding features reflect controlling axes that dictate community compositions. Using data from different animal hosts, organ sites, and microbial kingdoms of life, we show that SMbiot identifies a small number of host-specific latent variables that accurately capture the compositional variation in host associated microbial communities. By using the same latents to describe hosts’ phenotypic states and the host-associated microbiomes, we show that the latent space embedding is informed by host physiology as well as the associated microbiomes. Importantly, SMbiot enables the quantification of host phenotypic differences associated with altered microbial community compositions in a host-specific manner, underscoring the context specificity of host-microbiome associations. SMbiot can also predict missing host metadata or microbial community compositions. This way, SMbiot is a concise quantitative method to understand the low dimensional collective behavior of host-associated microbiomes.
Highlighter: an optogenetic actuator for light-mediated, high resolution gene expression control in plants
Authors: Larsen Bo , Hofmann Roberto , Camacho Ines S , Clarke Richard W , Lagarias J Clark , Jones Alex R , Jones Alexander M 
Published: October 2022

AbstractOptogenetic actuators have revolutionized the resolution at which we can assert control over biological processes in living systems. In plants, deployment of optogenetics is challenging due to the need for these light-responsive systems to maintain a single activation state in conventional horticultural environments with light-dark cycling. Furthermore, many available optogenetic actuators are based on plant photoreceptors that might crosstalk with endogenous signaling processes, while others depend on exogenously supplied cofactors. To overcome such challenges, we have developed Highlighter; a synthetic, light-gated gene expression system tailored forin plantafunction. Highlighter is based on the photoswitchable CcaS-CcaR system from cyanobacteria and is repurposed for plants as a fully genetically encoded system, engineered to photoswitch with the endogenous plant chromophore, phytochromobilin. We deployed Highlighter in transiently transformedNicotiana benthamianafor optogenetic control of fluorescent protein expression and innate immune responses. Using light to guide differential fluorescent protein expression in nuclei of neighboring cells, we demonstrate unprecedented spatiotemporal control of target gene expression. We furthermore regulate activation of plant immunity by modulating the spectral composition of white light, demonstrating optogenetic control of a biological process in horticultural light environments. Highlighter is a step forward for optogenetics in plants and a technology for high-resolution gene induction that will advance fundamental plant biology and provide new opportunities for crop improvement.
Intercellular crosstalk in adult dental pulp is mediated by heparin-binding growth factors Pleiotrophin and Midkine
Authors: Jiravejchakul Natnicha , Abe Gabriela L. , Loza Martin , Park Soyoung , Matangkasombut Ponpan , Sasaki Jun-Ichi , Imazato Satoshi , Diez Diego , Standley Daron M. 
Published: October 2022

AbstractIn-depth knowledge of the cellular and molecular composition of dental pulp (DP) and the crosstalk between DP cells that drive tissue homeostasis or regeneration are not well understood. To address these questions, we performed data analysis of publicly available single-cell transcriptomes of DP. This analysis revealed that DP resident fibroblasts have a unique gene expression profile when compared with fibroblasts from 5 other reference tissues: blood, bone marrow, adipose tissue, lung, and skin. Genes coded for heparin-binding growth-factors, pleiotrophin (PTN) and midkine (MDK), possessed the highest differential expression levels in DP fibroblasts. In addition, we identified extensive crosstalk between DP fibroblasts and several other DP cells, including Schwann cells, MSCs and odontoblasts. These findings suggest that fibroblast-derived growth factors regulate DP niches, and thus have a potential role as dental therapeutic targets.