Bringing Open Data to Whole Slide Imaging

Supplementary information associated with Besson et al. (2019) ECDP 2019 Faced with the need to support a growing number of whole slide imaging (WSI) file formats, our team has extended a long-standing community file format (OME-TIFF) for use in digital pathology. The format makes use of the core TIFF specification to store multi-resolution (or "pyramidal") representations of a single slide in a flexible, performant manner. Here we describe the structure of this format, its performance characteristics, as well as an open-source library support for reading and writing pyramidal OME-TIFFs

Christian Higher Education in Europe: A Historical Overview

The history of Christian higher education in Europe may be analyzed in terms of seven eras. From their medieval origins in scholasticism and the practical needs of students and rulers, universities passed through Renaissance humanism to a period of decay, yet remained substantially Christian in intent. The Enlightenment exercised a partially secularizing influence, and the neohumanist reaction against it also tended to dilute the faith. The recent era of the late 20th and early 21st centuries has been associated with the rise of postmodernism and the involvement of the state in the quest for relevance. A Christian response to contemporary circumstances is to engage with the cultural currents of the present day and, in drawing on the thought of John Henry Newman and Sir Walter Moberly, to ensure the integration of Christianity into higher education so that discussion of ultimate questions is informed by the Christian faith

Association of the T allele of an intronic single nucleotide polymorphism in the colony stimulating factor 1 receptor with Crohn's disease: a case-control study

BACKGROUND: Polymorphisms in several genes (NOD2, MDR1, SLC22A4) have been associated with susceptibility to Crohn's disease. Identification of the remaining Crohn's susceptibility genes is essential for the development of disease-specific targets for immunotherapy. Using gene expression analysis, we identified a differentially expressed gene on 5q33, the colony stimulating factor 1 receptor (CSF1R) gene, and hypothesized that it is a Crohn's susceptibility gene. The CSF1R gene is involved in monocyte to macrophage differentiation and in innate immunity. METHODS: Patients provided informed consent prior to entry into the study as approved by the Institutional Review Board at LSU Health Sciences Center. We performed forward and reverse sequencing of genomic DNA from 111 unrelated patients with Crohn's disease and 108 controls. We also stained paraffin-embedded, ileal and colonic tissue sections from patients with Crohn's disease and controls with a polyclonal antibody raised against the human CSF1R protein. RESULTS: A single nucleotide polymorphism (A2033T) near a Runx1 binding site in the eleventh intron of the colony stimulating factor 1 receptor was identified. The T allele of this single nucleotide polymorphism occurred in 27% of patients with Crohn's disease but in only 13% of controls (X(2 )= 6.74, p < 0.01, odds ratio (O.R.) = 2.49, 1.23 < O.R. < 5.01). Using immunohistochemistry, positive staining with a polyclonal antibody to CSF1R was observed in the superficial epithelium of ileal and colonic tissue sections. CONCLUSIONS: We conclude that the colony stimulating factor receptor 1 gene may be a susceptibility gene for Crohn's disease

Understanding uncertainties in future Colorado River streamflow

Artículo -- Universidad de Costa Rica. Centro de Investigaciones Geofísicas, 2014The Colorado River is the primary water source for more than 30 million people in the United States and Mexico. Recent studies that project streamflow changes in the Colorado River all project annual declines, but the magnitude of the projected decreases range from less than 10% to 45% by the mid-twenty-first century. To understand these differences, we address the questions the management community has raised: Why is there such a wide range of projections of impacts of future climate change on Colorado River streamflow, and how should this uncertainty be interpreted? We identify four major sources of disparities among studies that arise from both methodological and model differences. In order of importance, these are differences in 1) the global climate models (GCMs) and emission scenarios used; 2) the ability of land surface and atmospheric models to simulate properly the high-elevation runoff source areas; 3) the sensitivities of land surface hydrology models to precipitation and temperature changes; and 4) the methods used to statistically downscale GCM scenarios. In accounting for these differences, there is substantial evidence across studies that future Colorado River streamflow will be reduced under the current trajectories of anthropogenic greenhouse gas emissions because of a combination of strong temperature-induced runoff curtailment and reduced annual precipitation. Reconstructions of preinstrumental streamflows provide additional insights; the greatest risk to Colorado River streamflows is a multidecadal drought, like that observed in paleoreconstructions, exacerbated by a steady reduction in flows due to climate change. This could result in decades of sustained streamflows much lower than have been observed in the ~100 years of instrumental record.Universidad de Costa Rica. Centro de Investigaciones GeofísicasLamont-Doherty Earth Observatory of Columbia UniversityUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones Geofísicas (CIGEFI

Systematic Identification of Balanced Transposition Polymorphisms in Saccharomyces cerevisiae

High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism

Generation, Annotation and Analysis of First Large-Scale Expressed Sequence Tags from Developing Fiber of Gossypium barbadense L

BACKGROUND: Cotton fiber is the world's leading natural fiber used in the manufacture of textiles. Gossypium is also the model plant in the study of polyploidization, evolution, cell elongation, cell wall development, and cellulose biosynthesis. G. barbadense L. is an ideal candidate for providing new genetic variations useful to improve fiber quality for its superior properties. However, little is known about fiber development mechanisms of G. barbadense and only a few molecular resources are available in GenBank. METHODOLOGY AND PRINCIPAL FINDINGS: In total, 10,979 high-quality expressed sequence tags (ESTs) were generated from a normalized fiber cDNA library of G. barbadense. The ESTs were clustered and assembled into 5852 unigenes, consisting of 1492 contigs and 4360 singletons. The blastx result showed 2165 unigenes with significant similarity to known genes and 2687 unigenes with significant similarity to genes of predicted proteins. Functional classification revealed that unigenes were abundant in the functions of binding, catalytic activity, and metabolic pathways of carbohydrate, amino acid, energy, and lipids. The function motif/domain-related cytoskeleton and redox homeostasis were enriched. Among the 5852 unigenes, 282 and 736 unigenes were identified as potential cell wall biosynthesis and transcription factors, respectively. Furthermore, the relationships among cotton species or between cotton and other model plant systems were analyzed. Some putative species-specific unigenes of G. barbadense were highlighted. CONCLUSIONS/SIGNIFICANCE: The ESTs generated in this study are from the first large-scale EST project for G. barbadense and significantly enhance the number of G. barbadense ESTs in public databases. This knowledge will contribute to cotton improvements by studying fiber development mechanisms of G. barbadense, establishing a breeding program using marker-assisted selection, and discovering candidate genes related to important agronomic traits of cotton through oligonucleotide array. Our work will also provide important resources for comparative genomics, polyploidization, and genome evolution among Gossypium species