Single-cell and spatial sequencing application in pathology

Traditionally, diagnostic pathology uses histology representing structural alterations in a disease’s cells and tissues. In many cases, however, it is supplemented by other morphology-based methods such as immunohistochemistry and fluorescent in situ hybridization. Single-cell RNA sequencing (scRNA-seq) is one of the strategies that may help tackle the heterogeneous cells in a disease, but it does not usually provide histologic information. Spatial sequencing is designed to assign cell types, subtypes, or states according to the mRNA expression on a histological section by RNA sequencing. It can provide mRNA expressions not only of diseased cells, such as cancer cells but also of stromal cells, such as immune cells, fibroblasts, and vascular cells. In this review, we studied current methods of spatial transcriptome sequencing based on their technical backgrounds, tissue preparation, and analytic procedures. With the pathology examples, useful recommendations for pathologists who are just getting started to use spatial sequencing analysis in research are provided here. In addition, leveraging spatial sequencing by integration with scRNA-seq is reviewed. With the advantages of simultaneous histologic and single-cell information, spatial sequencing may give a molecular basis for pathological diagnosis, improve our understanding of diseases, and have potential clinical applications in prognostics and diagnostic pathology

Analogy, Spirituality and the Beatific Enjoyment of God: Bonaventure and the Doctrine of Image and Likneness

Thesis advisor: Stephen F. BrownThe dissertation explores Bonaventure’s understanding of the doctrine of image and likeness in terms of analogy, spirituality and the beatific enjoyment of God. The concept had a patristic background, and there were two trends in interpreting the concepts of image and likeness: one which distinguished the concepts of image and likeness, and one which identified both. Irenaeus made a distinction between the image and likeness of God, whereas Augustine identified them. The monastic authors such as Bernard of Clairvaux, Hugh of St. Victor, and Richard of St. Victor contributed to develop the doctrine of image and likeness. In this period, monastic theologians constructed the idea that the image is a natural and inseparable endowment from God, while likeness is a supernatural gift. In his De sacramentis, Hugh articulates an important and influential statement: Imago pertinet ad figuram, similitudo ad naturam. Many of the medieval theologians, including Bonaventure, considered Hugh’s concept useful to interpret the distinction between image and likeness. Also, the affective reading of Dionysius by Hugh and Richard inspired Bonaventure to construct the spiritual theology in terms of affective ideology: Assimilation to God is more a matter of love than knowledge. Peter Lombard’s composition of The Book of the Sentences opened the possibility to talk about the image-likeness doctrine in terms of ‘uti’ and ‘frui,’ and of ‘res’ and ‘signa.’ Bonaventure further developed Lombard’s ideas, and he explicitly connected the idea of uti and frui, i.e., fruitio Dei, with the doctrine of image and likeness, i.e., the doctrine of analogy. In the scholastic era, the doctrine of image and likeness of God nuanced a new tone in that the schoolmen discussed the doctrine in terms of causal similarity between Creator and creatures, or of the metaphysics of causation. In this theological atmosphere, Bonaventure now relates visio beatifica to the theological argument of whether there is any convenientia between radically unlike things, such as God and creatures. According to Bonaventure, there is a convenientia between God and human beings in terms of comparatio duorum ad invicem. God as the formal object of the human soul “expressed/imprinted” God’s divine nature in the created order, that is, similitudo expressa. This divine likeness is the efficient cause for the human beings’ aspiration/capacity for God. It is important to notice that Bonaventure’s doctrine of analogy is a ‘theological instrument’ that plays between the doctrine of analogy and the spiritual life. Itinerarium is a fine theological and spiritual treatise that shows how Bonaventure sketches the course of the soul’s journey in terms of the godlikeness in the order of creation: vestige, image and likeness. For Bonaventure, St. Francis, a vir hierarchicus, is an ‘exemplar’ of a person who completes this assimilative/ascending process of the journey into God, and he becomes a ‘divine exemplar’ or a ‘similitudo expressa,’ benefiting others to ascend the ladder into the enjoyment of God. As an angelic person, Francis “descends” to the created order reality and participates in God’s providential care for the well beings of creatures including human beings.Thesis (PhD) — Boston College, 2019.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Theology

Data-Morphic Analyzing Approach for Understanding a Tennis Racket: Comparison of Tennis Rackets in UH Tennis Club

The shapes in the beginner group are relatively moderate than other groups. Some similar shapes are found in the intermediate group while extremely sharp shapes appear in the advanced group. I believe the reason that advanced player's shapes are sharper is they understand well about a racket and they choose a racket in a way of maximizing their preference between control and power.Art, School o

Fast Hardware-Software Coverification by Optimistic Execution of Real Processor

To achieve fast verification of the software part of embedded system, we propose to run the target processor optimistically, which effectively reduces the synchronization overhead with other simulators. For the optimistic processor execution, we present a processor execution platform and state saving/restoration methods. We performed optimistic execution of ARM710A processor in the coverification of an IS-95 CDMA cellular phone system and obtained up to orders of magnitude higher performance compared with the case that the processor runs conservatively. 1. Introduction Verification of system functionality and timing is one of the most difficult and important aspects of System on a Chip (SoC) design. For many system design teams, verification takes 50% to 80% of the overall system design effort [1]. For fast verification of the hardware part of the system being designed, cycle-based simulators and high performance emulation systems have been widely used. For the verification of the s..

Fast Prototyping of an IS-95 CDMA Cellular Phone: a Case Study

This paper presents a case study on fast prototyping of a wireless CDMA cellular phone system. We set up a fast prototyping flow which aims at reducing the coverification time. We captured executable specifications of the system with Ptolemy and Polis tools. We developed a prototyping board, a board debugger which provides in-circuit emulation functions, and a debug agent which works as a debugger and cosimulation interface to the prototyping board. Using the debug agent and cosimulation interface stars in Ptolemy, we performed coverification of the system by executing the SW part on a real processor and the HW part on an FPGA while simulating the remaining part on Ptolemy