GraphMatch: Efficient Large-Scale Graph Construction for Structure from Motion

We present GraphMatch, an approximate yet efficient method for building the matching graph for large-scale structure-from-motion (SfM) pipelines. Unlike modern SfM pipelines that use vocabulary (Voc.) trees to quickly build the matching graph and avoid a costly brute-force search of matching image pairs, GraphMatch does not require an expensive offline pre-processing phase to construct a Voc. tree. Instead, GraphMatch leverages two priors that can predict which image pairs are likely to match, thereby making the matching process for SfM much more efficient. The first is a score computed from the distance between the Fisher vectors of any two images. The second prior is based on the graph distance between vertices in the underlying matching graph. GraphMatch combines these two priors into an iterative "sample-and-propagate" scheme similar to the PatchMatch algorithm. Its sampling stage uses Fisher similarity priors to guide the search for matching image pairs, while its propagation stage explores neighbors of matched pairs to find new ones with a high image similarity score. Our experiments show that GraphMatch finds the most image pairs as compared to competing, approximate methods while at the same time being the most efficient.Comment: Published at IEEE 3DV 201

Impact of Alu repeats on the evolution of human p53 binding sites

<p>Abstract</p> <p>Background</p> <p>The p53 tumor suppressor protein is involved in a complicated regulatory network, mediating expression of ~1000 human genes. Recent studies have shown that many p53 <it>in vivo </it>binding sites (BSs) reside in transposable repeats. The relationship between these BSs and functional p53 response elements (REs) remains unknown, however. We sought to understand whether the p53 REs also reside in transposable elements and particularly in the most-abundant Alu repeats.</p> <p>Results</p> <p>We have analyzed ~160 functional p53 REs identified so far and found that 24 of them occur in repeats. More than half of these repeat-associated REs reside in Alu elements. In addition, using a position weight matrix approach, we found ~400,000 potential p53 BSs in Alu elements genome-wide. Importantly, these putative BSs are located in the same regions of Alu repeats as the functional p53 REs - namely, in the vicinity of Boxes A/A' and B of the internal RNA polymerase III promoter. Earlier nucleosome-mapping experiments showed that the Boxes A/A' and B have a different chromatin environment, which is critical for the binding of p53 to DNA. Here, we compare the Alu-residing p53 sites with the corresponding Alu consensus sequences and conclude that the p53 sites likely evolved through two different mechanisms - the sites overlapping with the Boxes A/A' were generated by CG → TG mutations; the other sites apparently pre-existed in the progenitors of several Alu subfamilies, such as AluJo and AluSq. The binding affinity of p53 to the Alu-residing sites generally correlates with the age of Alu subfamilies, so that the strongest sites are embedded in the 'relatively young' Alu repeats.</p> <p>Conclusions</p> <p>The primate-specific Alu repeats play an important role in shaping the p53 regulatory network in the context of chromatin. One of the selective factors responsible for the frequent occurrence of Alu repeats in introns may be related to the p53-mediated regulation of Alu transcription, which, in turn, influences expression of the host genes.</p> <p>Reviewers</p> <p>This paper was reviewed by Igor B. Rogozin (nominated by Pavel A. Pevzner), Sandor Pongor, and I. King Jordan.</p

Filipino physician-turned nurses: A phenomenological study

Foreign nurses have augmented the United States nursing workforce. The Philippines has remained the world\u27s leading exporter of nurses, including the United States. More recently, a new phenomenon has emerged involving Filipino physicians who went back to school to take up nursing in the Philippines in order to migrate to foreign countries to work as nurses. The purpose of this study was to describe and to interpret the lived experiences of Filipino physician-turned nurses in the United States. Phenomenology was used as research design, with data obtained from a purposive sample of eight (8) self-identified physician-turned nurses in Las Vegas, Nevada. Participants were interviewed using a single, open-ended central question. The audio taped responses that described their lived experiences were eventually transcribed verbatim. To interpret their experiences, clusters of themes were then generated using the Colaizzi\u27s (1978) method of Phenomenological Inquiry. The results of the study revealed that the experiences of Filipino physician-turned nurses involved multidimensional issues, both in the contexts of emigration and a professional shift from physician to nurse. Being the first of its kind, this study will enlighten society of the lived experiences of Filipino physicians who compromise professional integrity by working as nurses just to emigrate to the United States. Furthermore, this research study will contribute to the existing literature on cross-cultural adaptation, particularly involving role compromise in an unfamiliar social and cultural context

A Comparative Analysis of Gene-Expression Data of Multiple Cancer Types

A comparative study of public gene-expression data of seven types of cancers (breast, colon, kidney, lung, pancreatic, prostate and stomach cancers) was conducted with the aim of deriving marker genes, along with associated pathways, that are either common to multiple types of cancers or specific to individual cancers. The analysis results indicate that (a) each of the seven cancer types can be distinguished from its corresponding control tissue based on the expression patterns of a small number of genes, e.g., 2, 3 or 4; (b) the expression patterns of some genes can distinguish multiple cancer types from their corresponding control tissues, potentially serving as general markers for all or some groups of cancers; (c) the proteins encoded by some of these genes are predicted to be blood secretory, thus providing potential cancer markers in blood; (d) the numbers of differentially expressed genes across different cancer types in comparison with their control tissues correlate well with the five-year survival rates associated with the individual cancers; and (e) some metabolic and signaling pathways are abnormally activated or deactivated across all cancer types, while other pathways are more specific to certain cancers or groups of cancers. The novel findings of this study offer considerable insight into these seven cancer types and have the potential to provide exciting new directions for diagnostic and therapeutic development

Analysis and Synthesis of Alternative Solutions to Environmental Problems Associated with Large-scale Projects

In this study the environmental problems in the large-scale project called "Ecology of the Angaro-Yenisei region" are addressed. A description of various approaches to assess the program of conservation and restoration of the Yenisei as the basis of the ecological potential of the Angaro-Yenisei region is presented. A justification is given for taking into account the uncertainty in such an assessment. The present study suggests three stages of assessment for different levels, macro-, meso- and microlevel. The estimates of the previous assessment level are the initial information for the lower level, which allows a gradually reduction of the degree of uncertainty. At the first stage, the goals of the program were developed and ranked by expert assessment methods. The second stage consisted in analyzing the National Project called "Ecology of Russia," composed of 11 interconnected federal projects. A mathematical model of the problem of optimal project management in conditions of uncertainty is presented. At the third stage, a hybrid model of assessing a large ecological project from the logical-descriptive model created at the first stage and the mathematical model of stage 2 is considered. Similar models, in the creation of which the authors took part, were used in the assessment of large-scale railway projects. More specifically, with the help of one of them, an analysis of the development of the Asian part of the Russian Federation was carried out by the Siberian branch of the Russian Academy of Sciences. In conclusion, the need of the use of mathematical methods at various stages of assessing large-scale environmental projects from their initiation to implementation is justifie

Hydrogen peroxide is a diffusible paracrine signal for the induction of epithelial cell death by activated myofibroblasts

Cell‐cell signaling roles for reactive oxygen species (ROS) generated in response to growth factors/cytokines in nonphagocytic cells are not well defined. In this study, we show that fibroblasts isolated from lungs of patients with idiopathic pulmonary fibrosis (IPF) generate extracellular hydrogen peroxide (H2O2) in response to the multifunctional cytokine, transforming growth factor‐β1 (TGF‐β1). In contrast, TGF‐β1 stimulation of small airway epithelial cells (SAECs) does not result in detectable levels of extracellular H2O2. IPF fibroblasts independently stimulated with TGF‐β1 induce loss of viability and death of overlying SAECs when cocultured in a compartmentalized Transwell system. These effects on SAECs are inhibited by the addition of catalase to the coculture system or by the selective enzymatic blockade of H2O2 production by IPF fibroblasts. IPF fibroblasts heterogeneously express α‐smooth muscle actin stress fibers, a marker of myofibroblast differentiation. Cellular localization of H2O2 by a fluorescent‐labeling strategy demonstrated that extracellular secretion of H2O2 is specific to the myofibroblast phenotype. Thus, myofibroblast secretion of H2O2 functions as a diffusible death signal for lung epithelial cells. This novel mechanism for intercellular ROS signaling may be important in physiological/pathophysiological processes characterized by regenerating epithelial cells and activated myofibroblasts.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154383/1/fsb2fj042882fje.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154383/2/fsb2fj042882fje-sup-0001.pd