Where people shop is not associated with the nutrient quality of packaged foods for any racial-ethnic group in the United States

Background: In the literature, it has been suggested that there are race-ethnic disparities in what Americans eat. In addition, some studies have shown that residents of African American and low-income neighborhoods have less access to grocery stores and supermarkets, which tend to stock healthier foods. However, it is unclear whether differences in food shopping patterns contribute to the poorer nutrient profile of food purchases made by racial-ethnic minorities

Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME†

Summary: Analysing large amounts of data generated by next-generation sequencing (NGS) technologies is difficult for researchers or clinicians without computational skills. They are often compelled to delegate this task to computer biologists working with command line utilities. The availability of easy-to-use tools will become essential with the generalization of NGS in research and diagnosis. It will enable investigators to handle much more of the analysis. Here, we describe Knime4Bio, a set of custom nodes for the KNIME (The Konstanz Information Miner) interactive graphical workbench, for the interpretation of large biological datasets. We demonstrate that this tool can be utilized to quickly retrieve previously published scientific findings

Response of FDG avid pelvic bone marrow to concurrent chemoradiation for anal cancer

BACKGROUND AND PURPOSE: To determine if suppression of active bone marrow, as defined on FDG PETCT, is seen in on-treatment imaging of anal cancer patients receiving concurrent chemoradiation. METHODS AND MATERIALS: Scans from 26 patients participating in the ART trial (full title: Anal squamous cell carcinoma: Investigation of functional imaging during chemoRadioTherapy), a single center observational study with FDG PETCT prior to radiotherapy and at fraction 8-10 of concurrent chemoradiation were analysed. Active bone marrow was contoured in both the pelvis and un-irradiated thoracic spine. SUV and volume of active bone marrow after 8-10 fractions of treatment were compared to baseline. Dose metrics to pelvic active bone marrow were extracted and compared to reduction in SUV/active bone marrow volume and to blood count nadir using linear regression. RESULTS: Suppression of active bone marrow is seen in the pelvis by a reduction in mean SUV and volume of active bone marrow after 8-10 fractions of treatment. Suppression is not seen in un-irradiated thoracic spine. Dose metrics were associated with reduced SUV and reduced volume of active bone marrow. Volume of active bone marrow receiving <20 Gy was associated with WCC/ANC nadir. 20 Gy was identified as the most likely clinically meaningful dose threshold for toxicity. Volume of active bone marrow receiving <20 Gy correlated to WCC and ANC with an increase of 100 cc being associated with an increase of 0.4 and 0.3 respectively. CONCLUSION: The effect of concurrent chemoradiation in suppression of active bone marrow is seen in on-treatment FDG PETCT scans. Chemotherapy appears well tolerated after 2 weeks of treatment

US Household Food Shopping Patterns: Dynamic Shifts Since 2000 And Socioeconomic Predictors

Under the assumption that differential food access might underlie nutritional disparities, programs and policies have focused on the need to build supermarkets in underserved areas, in an effort to improve dietary quality. However, there is limited evidence about which types of stores different income and race-ethnic households use. We used cross-sectional cluster analysis to derive shopping patterns from US households’ volume food purchases (Nielsen Homescan) by store from 2000–2012. Multinomial logistic regression identified household SES characteristics that were associated with shopping patterns in 2012. We found three shopping patterns: primary-grocery, primary-mass-merchandise, and combination cluster. In 2012, we found no income/race-ethnic differences for grocery cluster membership. However, low-income non-Hispanic blacks (vs. non-Hispanic whites) had a significantly lower probability of belonging to the mass-merchandise cluster. These varied shopping patterns must be considered in future policy initiatives. Further, it is important to continue studying the complex rationale for people’s food shopping patterns

Characterization of human mesothelin transcripts in ovarian and pancreatic cancer

BACKGROUND: Mesothelin is an attractive target for cancer immunotherapy due to its restricted expression in normal tissues and high level expression in several tumor types including ovarian and pancreatic adenocarcinomas. Three mesothelin transcript variants have been reported, but their relative expression in normal tissues and tumors has been poorly characterized. The goal of the present study was to clarify which mesothelin transcript variants are commonly expressed in human tumors. METHODS: Human genomic and EST nucleotide sequences in the public databases were used to evaluate sequences reported for the three mesothelin transcript variants in silico. Subsequently, RNA samples from normal ovary, ovarian and pancreatic carcinoma cell lines, and primary ovarian tumors were analyzed by reverse transcription-polymerase chain reaction (RT-PCR) and nucleotide sequencing to directly identify expressed transcripts. RESULTS: In silico comparisons of genomic DNA sequences with available EST sequences supported expression of mesothelin transcript variants 1 and 3, but there were no sequence matches for transcript variant 2. Newly-derived nucleotide sequences of RT-PCR products from tissues and cell lines corresponded to mesothelin transcript variant 1. Mesothelin transcript variant 2 was not detected. Transcript variant 3 was observed as a small percentage of total mesothelin amplification products from all studied cell lines and tissues. Fractionation of nuclear and cytoplasmic RNA indicated that variant 3 was present primarily in the nuclear fraction. Thus, mesothelin transcript variant 3 may represent incompletely processed hnRNA. CONCLUSION: Mesothelin transcript variant 1 represents the predominant mature mRNA species expressed by both normal and tumor cells. This conclusion should be important for future development of cancer immunotherapies, diagnostic tests, and gene microarray studies targeting mesothelin

Identity-by-descent filtering of exome sequence data for disease–gene identification in autosomal recessive disorders

Motivation: Next-generation sequencing and exome-capture technologies are currently revolutionizing the way geneticists screen for disease-causing mutations in rare Mendelian disorders. However, the identification of causal mutations is challenging due to the sheer number of variants that are identified in individual exomes. Although databases such as dbSNP or HapMap can be used to reduce the plethora of candidate genes by filtering out common variants, the remaining set of genes still remains on the order of dozens

Multiple shifts and fractional integration in the us and uk unemployment rates

This paper analyses the long-run behaviour of the US and UK unemployment rates by testing for possibly fractional orders of integration and multiple shifts using a sample of over 100 annual observations. The results show that the orders of integration are higher than 0 in both series, which implies long memory. If we assume that the underlying disturbances are white noise, the values are higher than 0.5, i.e., nonstationary. However, if the disturbances are autocorrelated, the orders of integration are in the interval (0, 0.5), implying stationarity and mean-reverting behaviour. Moreover, when multiple shifts are taken into account, unemployment is more persistent in the US than in the UK, implying the need for stronger policy action in the former to bring unemployment back to its original level