Moment of Glory

First prize, short story contes

Differential Gene Expression in Response to Hypoxia and Acidosis in Chest Wall Deformities and Chondrosarcoma

The importance of understanding how costal cartilage chondrocytes respond to stimuli such as oxidative stress and low pH has been largely overlooked in studies involving tissue culturing due to major differences between oxygen and pH levels during incubation and the natural environment of hyaline cartilage. Hyaline cartilage is avascular and naturally hypoxic which subsequently leads to increased glycolytic metabolism and ultimately causes a decrease in extracellular pH. To examine how healthy costal cartilage responds to these extreme growth conditions, we examined responses in three hyaline cartilage diseases. Our ability to identify the disease mechanisms responsible for pectus excavatum, pectus carinatum, and chondrosarcoma are limited by our understanding of how these mechanisms operate. This study aimed to determine the roles of hypoxia and extracellular acidosis on the expression of genes related to the hypoxia response pathway in costal cartilage chondrocytes, two pectus chest wall deformities, and the hyaline cartilage producing cancer, chondrosarcoma. Cells isolated from costal cartilage were incubated under four experimental conditions, where cultures were subjected to 24 hours of either hypoxia (5% oxygen) or normoxia, and 60 seconds of acidic media (pH5.5) or kept at neutral pH (pH 7.2) just prior to RNA extraction. Expression levels for 84 genes were tested by RT-qPCR to determine genes of interest within the hypoxia response pathway. Two genes, factor 3 F3 and lysyl oxidase LOX, were chosen based on high fold change within the preliminary study; two replicate experiments were repeated for a total of 12 patient samples. Our analysis showed no significant change in any cell type compared to the control. However, the control and PC sample groups showed significant upregulation of both F3 (Control, p=0.0001, PC, p=0.0026) and LOX (Control, p=0.0009, PC, p=0.0047) within the cell type in response to hypoxia, but PE and JJ012 samples showed no significant response. Low pH had no significant effect on expression levels in any cell type. Further study of how cellular response mechanisms to hypoxia and acidosis in healthy and diseased hyaline cartilage is required to fill knowledge gaps and create understanding for new therapies to treat pectus chest wall deformities or chondrosarcoma cancer

[X]uniqMAP: unique gene sequence regions in the human and mouse genomes

BACKGROUND: Current approaches for genome-wise functional analyses, such as microarray and RNA interference studies, rely on the specificity of oligonucleotide sequences to selectively target cellular transcripts. The design of specific oligos involves the determination of unique DNA regions in the gene/transcripts of interest from the targeted organism. This process is tedious, time consuming and it does not scale up for high-throughput studies. DESCRIPTION: Taking advantage of the availability of complete genome sequence information for mouse and human, the most widely used systems for the study of mammalian genetics, we have built a database, [X]uniqMAP, that stores the precalculated unique regions for all transcripts of these two organisms. For each gene, the database discriminates between those unique regions that are shared by all transcripts and those exclusive to single transcripts. In addition, it also provides those unique regions that are shared between orthologous genes from the two organisms. The database is updated regularly to reflect changes in genome assemblies and gene builds. CONCLUSION: Over 85% of genes have unique regions at least 19 bases long, with the majority being unique over 60% of their lengths. 14482 human genes share exactly at least a unique region with mouse genes, though such regions are typically under 40 bases long. The full data are publicly accessible online both interactively and for download. They should facilitate (i) the design of probes, primers and siRNAs for both small- and large-scale projects; and (ii) the identification of regions for the design of oligos that could be re-used to target equivalent gene/transcripts from human and mouse

Parameter estimation in pair hidden Markov models

This paper deals with parameter estimation in pair hidden Markov models (pair-HMMs). We first provide a rigorous formalism for these models and discuss possible definitions of likelihoods. The model being biologically motivated, some restrictions with respect to the full parameter space naturally occur. Existence of two different Information divergence rates is established and divergence property (namely positivity at values different from the true one) is shown under additional assumptions. This yields consistency for the parameter in parametrization schemes for which the divergence property holds. Simulations illustrate different cases which are not covered by our results.Comment: corrected typo

Depression, Relationship Quality, and Couples’ Demand/Withdraw and Demand/Submit Sequential Interactions

This study investigated the associations among depression, relationship quality, and demand/withdraw and demand/submit behavior in couples’ conflict interactions. Two 10-min conflict interactions were coded for each couple (N = 97) using Structural Analysis of Social Behavior (SASB; Benjamin, 1979a, 1987, 2000a). Depression was assessed categorically (via the presence of depressive disorders) and dimensionally (via symptom reports). Results revealed that relationship quality was negatively associated with demanding behavior, as well as receiving submissive or withdrawing behavior from one’s partner. Relationship quality was positively associated with withdrawal. Demanding behavior was positively associated with women’s depression symptoms but negatively associated with men’s depression symptoms. Sequential analysis revealed couples’ behavior was highly stable across time. Initiation of demand/withdraw and demand/submit sequences were negatively associated with partners’ relationship adjustment. Female demand/male withdraw was positively associated with men’s depression diagnosis. Results underscore the importance of sequential analysis when investigating associations among depression, relationship quality, and couples’ interpersonal behavior

Workers\u27 Compensation and Injury Duration: Evidence from a Natural Experiment

This paper examines the effect of workers\u27 compensation on time out of work. It introduces a natural experiment approach of comparing individuals injured before and after increases in the maximum weekly benefit amount. The increases examined in Kentucky and Michigan raised the benefit amount for high-earnings individuals by approximately 50 percent, while low-earnings individuals, who were unaffected by the benefit maximum, did not experience a change in their incentives. Time out of work increased for those eligible for the higher benefits and remained unchanged for those whose benefits were constant. The estimated duration elasticities are clustered around 0.3-0.4

A Combined Digital-Analog Tracker for Terrestrial Applications

A combined Digital-Analog Tracker is suggested to allow maximum efficiency in a solar-electrical energy converter, utilizing a twelve-foot parabolic collector. The analog tracker compares solar beam radiation to ambient (diffuse) light to obtain optimum placement of the collector when the sun is visible. The digital portion of the tracker utilizes a wired program which derives information on solar position from a non-volatile random-access semiconductor memory. This arrangement allows accurate mapping of the sun even when the sun is obscured by atmospheric phenomena which would make mapping impossible