Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion.

The advent of cell culture-based methods for the establishment and expansion of human corneal endothelial cells (CEnC) has provided a source of transplantable corneal endothelium, with a significant potential to challenge the one donor-one recipient paradigm. However, concerns over cell identity remain, and a comprehensive characterization of the cultured CEnC across serial passages has not been performed. To this end, we compared two established CEnC culture methods by assessing the transcriptomic changes that occur during in vitro expansion. In confluent monolayers, low mitogenic culture conditions preserved corneal endothelial cell state identity better than culture in high mitogenic conditions. Expansion by continuous passaging induced replicative cell senescence. Transcriptomic analysis of the senescent phenotype identified a cell senescence signature distinct for CEnC. We identified activation of both classic and new cell signaling pathways that may be targeted to prevent senescence, a significant barrier to realizing the potential clinical utility of in vitro expansion

An Ontology for Product-Service Systems

Industries are transforming their business strategy from a product-centric to a more service-centric nature by bundling products and services into integrated solutions to enhance the relationship between their customers. Since Product- Service Systems design research is currently at a rudimentary stage, the development of a robust ontology for this area would be helpful. The advantages of a standardized ontology are that it could help researchers and practitioners to communicate their views without ambiguity and thus encourage the conception and implementation of useful methods and tools. In this paper, an initial structure of a PSS ontology from the design perspective is proposed and evaluated

Assumption 0 analysis: comparative phylogenetic studies in the age of complexity

Darwin's panoramic view of biology encompassed two metaphors: the phylogenetic tree, pointing to relatively linear (and divergent) complexity, and the tangled bank, pointing to reticulated (and convergent) complexity. The emergence of phylogenetic systematics half a century ago made it possible to investigate linear complexity in biology. Assumption 0, first proposed in 1986, is not needed for cases of simple evolutionary patterns, but must be invoked when there are complex evolutionary patterns whose hallmark is reticulated relationships. A corollary of Assumption 0, the duplication convention, was proposed in 1990, permitting standard phylogenetic systematic ontology to be used in discovering reticulated evolutionary histories. In 2004, a new algorithm, phylogenetic analysis for comparing trees (PACT), was developed specifically for use in analyses invoking Assumption 0. PACT can help discern complex evolutionary explanations for historical biogeographical, coevolutionary, phylogenetic, and tokogenetic processe

Gene expression of endangered coral (Orbicella spp.) in flower garden banks National Marine Sanctuary after Hurricane Harvey

About 190 km south of the Texas–Louisiana border, the East and West Flower Garden Banks (FGB) have maintained > 50% coral cover with infrequent and minor incidents of disease or bleaching since monitoring began in the 1970s. However, a mortality event, affecting 5.6 ha (2.6% of the area) of the East FGB, occurred in late July 2016 and coincided with storm-generated freshwater runoff extending offshore and over the reef system. To capture the immediate effects of storm-driven freshwater runoff on coral and symbiont physiology, we leveraged the heavy rainfall associated with Hurricane Harvey in late August 2017 by sampling FGB corals at two time points: September 2017, when surface water salinity was reduced (∼34 ppt); and 1 month later when salinity had returned to typical levels (∼36 ppt in October 2017). Tissue samples (N = 47) collected midday were immediately preserved for gene expression profiling from two congeneric coral species (Orbicella faveolata and Orbicella franksi) from the East and West FGB to determine the physiological consequences of storm-derived runoff. In the coral, differences between host species and sampling time points accounted for the majority of differentially expressed genes. Gene ontology enrichment for genes differentially expressed immediately after Hurricane Harvey indicated increases in cellular oxidative stress responses. Although tissue loss was not observed on FGB reefs following Hurricane Harvey, our results suggest that poor water quality following this storm caused FGB corals to experience sub-lethal stress. We also found dramatic expression differences across sampling time points in the coral’s algal symbiont, Breviolum minutum. Some of these differentially expressed genes may be involved in the symbionts’ response to changing environments, including a group of differentially expressed post-transcriptional RNA modification genes. In this study, we cannot disentangle the effects of reduced salinity from the collection time point, so these expression patterns could also be related to seasonality. These findings highlight the urgent need for continued monitoring of these reef systems to establish a baseline for gene expression of healthy corals in the FGB system across seasons, as well as the need for integrated solutions to manage stormwater runoff in the Gulf of Mexico.https://www.frontiersin.org/articles/10.3389/fmars.2019.00672/fullPublished versionPublished versio

Mindful reflexivity: Unpacking the process of transformative learning in mindfulness and discernment

Can spiritual practice encourage transformative learning? In this article, we unpack how spiritual practices from the Buddhist tradition—mindfulness—and the Quaker tradition—discernment—encourage the attainment of moral reflexivity and the capacity to transform self in individual and relational organizational contexts, respectively. We also show how moral reflexivity and self-transformation are mutually reinforcing and promote a transformational cycle of management learning. We propose that “mindful reflexivity”, a foundational model of spiritually informed moral reflexivity, can contribute to new ways of management learning through its context sensitivity and ethical orientation to foster the kinds of reflexivity needed for responsible management. Our article concludes with implications for management learning theory and practice, and we offer pathways for future research

Negotiating with a logical-linguistic protocol in a dialogical framework

This book is the result of years of reflection. Some time ago, while working in commodities, the author felt how difficult it was to decide the order in which to use arguments during a negotiation process. What would happen if we translated the arguments into cards and played them according to the rules of the Bridge game? The results were impressive. There was potential for improvement in the negotiation process. The investigation went deeper, exploring players, cards, deals and the information concealed in the players´ announcements, in the cards and in the deals. This new angle brought the research to NeuroLinguistic Patterns and cryptic languages, such as Russian Cards. In the following pages, the author shares her discovery of a new application for Logical Dialogues: Negotiations, tackled from basic linguistic structures placed under a dialogue form as a cognitive system which ‘understands’ natural language, with the aim to solve conflicts and even to serve peace

High-resolution mapping of cancer cell networks using co-functional interactions.

Powerful new technologies for perturbing genetic elements have recently expanded the study of genetic interactions in model systems ranging from yeast to human cell lines. However, technical artifacts can confound signal across genetic screens and limit the immense potential of parallel screening approaches. To address this problem, we devised a novel PCA-based method for correcting genome-wide screening data, bolstering the sensitivity and specificity of detection for genetic interactions. Applying this strategy to a set of 436 whole genome CRISPR screens, we report more than 1.5 million pairs of correlated "co-functional" genes that provide finer-scale information about cell compartments, biological pathways, and protein complexes than traditional gene sets. Lastly, we employed a gene community detection approach to implicate core genes for cancer growth and compress signal from functionally related genes in the same community into a single score. This work establishes new algorithms for probing cancer cell networks and motivates the acquisition of further CRISPR screen data across diverse genotypes and cell types to further resolve complex cellular processes

Extraction of ontology and semantic web information from online business reports

CAINES, Content Analysis and INformation Extraction System, employs an information extraction (IE) methodology to extract unstructured text from the Web. It can create an ontology and a Semantic Web. This research is different from traditional IE systems in that CAINES examines the syntactic and semantic relationships within unstructured text of online business reports. Using CAINES provides more relevant results than manual searching or standard keyword searching. Over most extraction systems, CAINES extensively uses information extraction from natural language, Key Words in Context (KWIC), and semantic analysis. A total of 21 online business reports, averaging about 100 pages long, were used in this study. Based on financial expert opinions, extraction rules were created to extract information, an ontology, and a Semantic Web of data from financial reports. Using CAINES, one can extract information about global and domestic market conditions, market condition impacts, and information about the business outlook. A Semantic Web was created from Merrill Lynch reports, 107,533 rows of data, and displays information regarding mergers, acquisitions, and business segment news between 2007 and 2009. User testing of CAINES resulted in recall of 85.91%, precision of 87.16%, and an F-measure of 86.46%. Speed with CAINES was also greater than manually extracting information. Users agree that CAINES quickly and easily extracts unstructured information from financial reports on the EDGAR database