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Background Colorectal cancer (CRC) is the third most common cancer in the United States, and the second leading cause of cancer death. Comorbidity network analyses of CRC can help understanding of the illness progression. About 10%-30% of patients have a family history of CRC that suggests a hereditary contribution, including pathogenic variants of genes. The goal was to identify comorbidities associated with CRC and to discover pathogenic variants of genes that could be connected to CRC and comorbidity diseases. Results A novel model is developed based on comorbidity networks, to study progression of CRC. The model was developed on the HCUP, SID California inpatient database for a period of 9 years (2003-2011). Comorbidity networks, and Venn diagrams show probabilities of occurrence of comorbidities associated with different stages of CRC. Ranked lists of comorbidities (more than 5,800) were utilized for text mining of PubMed and expert curated sources (DisGeNet), to identify genes associated with CRC. Associations between 1,940 different genes and CRC were extracted from PubMed. 150 different genes are associated with CRC in DisGeNet. 96 genes are present in both sources (PubMed and curated sources). The most mentioned gene associated with CRC were: TP53 (241 abstracts in PubMed), APC (115), and KRAS (106). All 3 genes had DisGeNet scores of 0.5. Two more genes (MLH1 – 98 abstracts and TGFBR2 - 18 abstracts) had the same DisGeNet scores. PPARG gene (43 abstracts) had DisGeNet score of 0.6. Genes described on the cancer.gov website were found on PubMed too. MUTYH was described in association with CRC in 7 abstracts, MSH6 in 25 abstracts, PMS2 in 11, EPCAM in 10, POLD1 in 4, BMPR1A in 3, SMAD4 in 15, PTEN in 25 and STK11 in 8 PubMed abstracts. Lists of associations of the six most common genes and comorbidities of CRC were also created. Conclusions Results of the study could be considered as a novelty contributing to better understanding of risk factors (genes, comorbidities) for the development of CRC. Genetic findings could lead to the improvement of guidelines for genetic testing of patients that are at increased risk to develop CRC.

Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body.

Using dilution-to-extinction cultivation, we isolated a strain affiliated with the PS1 clade from surface waters of the Red Sea. Strain RS24 represents the second isolate of this group of marine Alphaproteobacteria after IMCC14465 that was isolated from the East (Japan) Sea. The PS1 clade is a sister group to the OCS116 clade, together forming a putatively novel order closely related to Rhizobiales. While most genomic features and most of the genetic content are conserved between RS24 and IMCC14465, their average nucleotide identity (ANI) is < 81%, suggesting two distinct species of the PS1 clade. Next to encoding two different variants of proteorhodopsin genes, they also harbor several unique genomic islands that contain genes related to degradation of aromatic compounds in IMCC14465 and in polymer degradation in RS24, possibly reflecting the physicochemical differences in the environment they were isolated from. No clear differences in abundance of the genomic content of either strain could be found in fragment recruitment analyses using different metagenomic datasets, in which both genomes were detectable albeit as minor part of the communities. The comparative genomic analysis of both isolates of the PS1 clade and the fragment recruitment analysis provide first insights into the ecology of this group.

Economists have always found it difficult to investigate the demand for the automobile good due to its heterogeneity. In this paper, the automobile is treated as a differentiated product, and a two-step approach is used to estimate a system of structural demand equations for automobile attributes. The obtained results are statistically sound and in conformity with theoretical expectations. This should be taken as an indication of the validity and robustness of the procedure used in this analysis.

This paper uses a two-stage cost function model to analyse substitution possibilities among inputs in the production of urban housing. Aggregate price indexes for groups of inputs are generated in the first stage, and then used in the estimation of the aggregate cost function in the second stage. The procedure is valid under the assumption of weak separability. The use of flexible functional forms at both stages allowed the analysis to be carried out by imposing fewer restrictions as a part of the maintained hypothesis than has been the case in the previous literature. The findings are consistent with the postulates of cost-minimising factor demand theory.

This paper tests for the existence of short-run equilibrium in the urban housing market in Metropolitan Toronto. The alternative hypothesis is the housing market segmented with respect to locational and structural attributes. We found insignificant differences in attribute prices across hypothesized submarkets. This implies that an unstratified hedonic price regressions model, based on the assumption of short-run equilibrium, is equally efficient in the analysis of housing prices as a model based on a number of subsamples stratified along lines of segmentation.

This paper uses cost functions to test the hypothesis of constancy of the elasticity of substitution among land and capital inputs in the production of single-family housing. The findings suggest that the substitution parameter varies over the range of the sample. The hypothesis of homotheticity in the production is also rejected. This implies that the CES and Cobb–Douglas production functions are not suitable for urban housing production modelling. The analysis has been carried out by imposing much weaker restrictions as a part of the maintained hypotheses than has been the case in the recent literature.

In this paper, we have empirically estimated demand equations for housing attributes, using a two-step approach in conformity with the procedure proposed by Sherwin Rosen. The identification problem inherent in Rosen's procedure has been avoided by estimating separate equations for distinct market segments in the first step. The estimates of the demand functions obtained in the second step are consistent with theoretical expectations.

This paper uses a two-step approach to estimate a system of structural demand equations for housing attributes. Estimation of a hedonic price regression, in the first step, yields implicit prices for housing attributes for the Toronto Metropolitan area in 1978, which are then used to estimate the expenditure share equations derived from the indirect translog utility function. Empirical results indicate that the composite housing attributes (used in the second stage model) are own-price elastic, while an examination of cross price relationships reveals that these attributes are reasonably substitutable.

The purpose of this paper is to present some empirical findings on the impact of accessibility (distance) on theatre going in Toronto. The importance of the analysis should not be limited to this specialized urban function only. Baumol and Bowen (1966) provide an in-depth analysis of theatre and performing arts audiences. They find that characteristics of a theatre audience are very similar to the characteristics of a performing arts audience. In general, theatre going, then, can serve as a good proxy for the performing arts. Therefore, the analysis can be of assistance in providing an objective basis for the investigation of the effects of commuting trips made by performing arts audiences on the choice of residential location. The performing arts trips form a part of the nonwork Central Business District (CBD) trips. We postulate that the residential location decisions of consumers with strong preferences for performing arts are influenced by the easy accessibility to this type of consumption in terms of the time and money cost of travel. Consequently, the results of this analysis can be used to draw inferences about the likely impact of performing arts trips on residential location.

The objective of this paper is to investigate the role of marketing competition in the NorthAmerican automobile market. This is accomplished by estimating a market-share demand function. The main difficulty with the analysis of demand for automobiles is heterogeneity of model types. Quality differences among different models, both at a point in time and through time cannot be ignored, since price and sales depend on them. One way to remedy this situation is to apply the hedonic method by regressing the price of a model on its characteristics. In this way, the implicit prices for each of the qualitative attributes are derived and then used, free of quality-differences, in the second stage estimation of a market-share demand function. There has been considerable interest in estimating demand functions for automobiles. However, most of the previous research has focused on total automobile demand. In this approach, equations on total sales are estimated without taking into account differences in quality characteristics of different model types. These studies usually relate the depreciation of the service level of the currently held stock of automobiles to the demand for new stock. This leads to a very general stock adjustment [7] or generalized acceleration framework [10]. The best known time-series studies of the aggregate automobile demand using different variants of this approach are those of Chow [2], Suits [15], Wykoff [19], and Westin [18]. The estimates of price elasticities from these studies are about - 1, and income elasticities range from 1.5 to 4. Previous research on automobile demand allowing for qualitative differences in characteristics among different models is much less extensive. The most important research effort in this direction is the paper by Cowling and Cubbin [4]. They explained market-share movements for different car manufacturers by changes in quality adjusted prices using data from England for the period 1957-1968. Their quality adjusted price vector is proxied by the residuals from hedonic price regressions, using the data on manufacturer's models. The idea that the residuals from the regression of prices of differentiated goods on their qualitative attributes are the quality adjusted prices, was suggested by Griliches [8]. Cowling and Cubbin used, as their quality-adjusted price for a specific manufacturing firm, the mean residual computed by taking into account all the models offered by