1,721,056 research outputs found
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Demystifying the Choroid Plexus
Full text linkAs biomedical technology advances and studies uncover new forms of elucidating the underlying mechanisms of our brain, we can begin to study the brain’s components, development, function, and health. This thesis will focus on the choroid plexus (CP), a tissue essential for the development and maintenance of the brain. The choroid plexus is composed of cuboidal epithelial cells known was choroid plexus epithelial cells (CPEC). CPEC are responsible for cerebrospinal fluid (CSF) secretion and form the blood cerebrospinal fluid barrier. Over and under production of CSF production have been linked to various mental disorders. Furthermore, it has been speculated that accelerated CPEC atrophy leads to a reduction in CSF and protein secretion, a phenomenon described in Alzheimer's Disease (AD). Despite CPEC’s critical role, very little has been done to study the normal CPEC function. In this thesis, CPEC morphology, protein expression, and barrier properties will be explored. This body of work aims to demystify normal CPEC function in hopes that it will serve as foundation for future pathological studies
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Investigating the mysteries of human choroid plexus development in varying physiological states using pluripotent stem cells
No full textAs the interface between the blood and cerebrospinal fluid, the choroid plexus (ChP) mediates body-brain homeostasis and has broad potential for CNS regenerative medicine. Despite this, little is known about the human ChP or its epithelial cells (CPECs), which have been considered a uniform cell type. Based on an earlier proof-of-concept method, we devised a simple, efficient, and scalable protocol for CPEC differentiation from human pluripotent stem cells. Our 2D culture method shows success across multiple cell lines including iPSCs. The derived CPECs (dCPECs) developed canonical CPEC properties and functions in the absence of mesenchymal elements. The derived cells were them applied to wo branches of studies: modeling physiological development and heterogeneity of human CPECs and non-physiological diseases that have developmental origins. Developmental studies through single dCPEC transcriptomes across time, which increasingly correlated well with fetal CPEC transcriptomes, revealed a direct dCPEC origin from neuroepithelial cells that also produced neurons and neural progenitors. Transcriptomic analysis also identified dCPEC diversifications at early and later stages into subtypes enriched for anabolic-secretory (type1a), catabolic-absorptive (type1b), and ciliogenesis pathways (type2). Additionally, the subtypes were present at different stages of development, with the type 1 and 2 CPECs present until mid-gestation where only type 1 CPECs continue until late gestation where this population branches into type 1a and 1b CPECs. Our time course study has revealed novel roles of human CPECs and positioned them in a dynamic role in shaping the environment of the developing human brain. Disease modeling applications using patient derived iPSCs, have highlighted the possible relationship between CPECs and different neurological conditions. Diseases that have a developmental origin, such as mitochondria defect diseases and Alzheimer’s disease, have been modeled in our 2D cultures and show a negative effect on CPEC functions, and in the case of modeling Alzheimer’s disease, a differential effect on one CPEC subtype. These findings establish a robust human CPEC model system for basic studies and regenerative medicine applications while revealing CPEC subtype diversifications during prenatal human development and subtype specific effects in neurodegenerative diseases
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Manual and deep learning characterization of common human choroid plexus pathologies
No full textThe choroid plexus (ChP) plays an important role in brain homeostasis and its dysfunction may have a role in brain aging and diseases such as Alzheimer’s disease (AD). However, many aging and disease-related changes within the ChP are understudied. In particular, pathologies known to affect the ChP, such as Biondi bodies (BB), lack thorough, systematic characterization. To address this knowledge gap, we have developed both manual and deep-learning (DL) approaches to characterize two common ChP pathologies: BBs and fibrosis. We developed a rigorous manual counting methodology to measure the prevalence, load, and size of each pathology and used this data to train DL models based on ResNet, RetinaNet, and UNet architectures. Using these models, we quantified the prevalence, load, and spatial distribution of these pathologies using thioflavin S and H&E-stained sections of ChP autopsy tissue from over 100 individuals across human lifespan and disease. Our manual analysis found that BB and fibrosis significantly increase with age, can appear quite early in life, and that BBs can spatially cluster within the ChP. Additionally, manual quantification of BB morphology revealed variations across individuals as well as a near-significant association with AD. DL models trained from our manual analysis performed well compared to human annotators, recapitulating findings from our manual studies, and in the case of fibrosis, improved the quality of annotations. These models were then used to measure BB load and map the spatial distribution of BB, fibrosis, and large lipid vesicles within the ChP, revealing increases of BB load with age as well as spatial clustering of all pathologies in nearly all samples studied. Clustering of BBs was also seen at the cell-cell level, suggesting prion-like spread. Lastly, spatial analysis of fibrosis alongside large lipid vacuoles revealed a negative spatial interaction. Altogether these results show that multiple ChP pathologies increasingly impact the ChP as we age, likely reflecting ChP dysfunction, and highlight DL models as a valuable tool for the study of ChP pathology
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Redefining the morphogen hypothesis: BMP-FGF interactions and kinetics in the developing telencephalon
Full text linkNeural development is a highly orchestrated process, patterning of naïve tissue into highly evolved structures with multiple cell types and functions is highly complex and not fully understood. Conventional understanding of pattern formation assumes extrinsic morphogen concentration to be the sole determining factor. However, this perspective has been challenged recently, raising the possibility of additional mechanisms at play.In this dissertation, I address the process of patterning and neurodevelopment by first understanding the morphogens involved in patterning the developing telencephalon and their interactions, and secondly by studying the kinetics and signaling pathway of these morphogens and how they implicate patterning and border formation.My studies demonstrated that BMP and FGF signaling pathways interact in a mutually inhibitory fashion at both the population level and single cell level. Ixviidetermined that BMP signaling exhibited fast activation and slow deactivation kinetics, whereas FGF signaling displayed slow acting kinetics. Based on these findings, I determined the advantages of such network design in tissue patterning and robust border formation. I demonstrated that patterning is a dynamic process that occurs over time. I introduced the notion of temporal integration in patterning the developing telencephalon, challenging the canonical morphogen theory, which states that gene expression and cell fate decisions are based on morphogen concentration alone. Lastly, I discovered that a slow and integrative system is robust to perturbations, where a transient disruption of signaling leads to developmental delay with eventual catch up recovery.Taken together, my findings have defined the interaction between BMPs and FGFs in the developing telencephalon, demonstrated the advantages of different signaling kinetics, and presented a novel mode of interaction between morphogens that is likely to be a general phenomenon. I have demonstrated the importance of studying patterning as a dynamic process, demonstrating the importance of temporal integration, thereby redefining the current understanding of patterning of naïve tissues by morphogens
A hybrid microfluidic-vacuum device for direct interfacing with conventional cell culture methods
Full text linkAbstract Background Microfluidics is an enabling technology with a number of advantages over traditional tissue culture methods when precise control of cellular microenvironment is required. However, there are a number of practical and technical limitations that impede wider implementation in routine biomedical research. Specialized equipment and protocols required for fabrication and setting up microfluidic experiments present hurdles for routine use by most biology laboratories. Results We have developed and validated a novel microfluidic device that can directly interface with conventional tissue culture methods to generate and maintain controlled soluble environments in a Petri dish. It incorporates separate sets of fluidic channels and vacuum networks on a single device that allows reversible application of microfluidic gradients onto wet cell culture surfaces. Stable, precise concentration gradients of soluble factors were generated using simple microfluidic channels that were attached to a perfusion system. We successfully demonstrated real-time optical live/dead cell imaging of neural stem cells exposed to a hydrogen peroxide gradient and chemotaxis of metastatic breast cancer cells in a growth factor gradient. Conclusion This paper describes the design and application of a versatile microfluidic device that can directly interface with conventional cell culture methods. This platform provides a simple yet versatile tool for incorporating the advantages of a microfluidic approach to biological assays without changing established tissue culture protocols.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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