ZoomQuant: An application for the quantitation of stable isotope labeled peptides

The main goal of comparative proteomics is the quantitation of the differences in abundance of many proteins between two different biological samples in a single experiment. By differentially labeling the peptides from the two samples and combining them in a single analysis, relative ratios of protein abundance can be accurately determined. Protease catalyzed 18O exchange is a simple method to differentially label peptides, but the lack of robust software tools to analyze the data from mass spectra of 18O labeled peptides generated by common ion trap mass spectrometers has been a limitation. ZoomQuant is a stand-alone computational tool that analyzes the mass spectra of 18O labeled peptides from ion trap instruments and determines relative abundance ratios between two samples. Starting with a filtered list of candidate peptides that have been successfully identified by Sequest, ZoomQuant analyzes the isotopic forms of the peptides using high-resolution zoom scan spectrum data. The theoretical isotope distribution is determined from the peptide sequence and is used to deconvolute the peak areas associated with the unlabeled, partially labeled, and fully labeled species. The ratio between the labeled and unlabeled peptides is then calculated using several different methods. ZoomQuant’s graphical user interface allows the user to view and adjust the parameters for peak calling and quantitation and select which peptides should contribute to the overall abundance ratio calculation. Finally, ZoomQuant generates a summary report of the relative abundance of the peptides identified in the two samples

Textiles as Material Gestalt: Cloth as a Catalyst in the Co-designing Process

Textiles is the common language within Emotional Fit, a collaborative research project investigating a person-centred, sustainable approach to fashion for an ageing female demographic (55+). Through the co-designing of a collection of research tools, textiles have acted as a material gestalt for exploring our research participants' identities by tracing their embodied knowledge of fashionable dress. The methodology merges Interpretative Phenomenological Analysis, co-design and a simultaneous approach to textile and garment design. Based on an enhanced understanding of our participants textile preferences, particular fabric qualities have catalysed silhouettes, through live draping and geometric pattern cutting to accommodate multiple body shapes and customisation. Printedtextiles have also been digitally crafted in response to the contours of the garment and body and personal narratives of wear. Sensorial and tactile interactions have informed the engineering and scaling of patterns within zero-waste volumes. The article considers the functional and aesthetic role of textiles

Increased Rate of Hospitalization for Diabetes and Residential Proximity of Hazardous Waste Sites

BACKGROUND: Epidemiologic studies suggest that there may be an association between environmental exposure to persistent organic pollutants (POPs) and diabetes. OBJECTIVE: The aim of this study was to test the hypothesis that residential proximity to POP-contaminated waste sites result in increased rates of hospitalization for diabetes. METHODS: We determined the number of hospitalized patients 25–74 years of age diagnosed with diabetes in New York State exclusive of New York City for the years 1993–2000. Descriptive statistics and negative binomial regression were used to compare diabetes hospitalization rates in individuals who resided in ZIP codes containing or abutting hazardous waste sites containing POPs (“POP” sites); ZIP codes containing hazardous waste sites but with wastes other than POPs (“other” sites); and ZIP codes without any identified hazardous waste sites (“clean” sites). RESULTS: Compared with the hospitalization rates for diabetes in clean sites, the rate ratios for diabetes discharges for people residing in POP sites and “other” sites, after adjustment for potential confounders were 1.23 [95% confidence interval (CI), 1.15–1.32] and 1.25 (95% CI, 1.16–1.34), respectively. In a subset of POP sites along the Hudson River, where there is higher income, less smoking, better diet, and more exercise, the rate ratio was 1.36 (95% CI, 1.26–1.47) compared to clean sites. CONCLUSIONS: After controlling for major confounders, we found a statistically significant increase in the rate of hospitalization for diabetes among the population residing in the ZIP codes containing toxic waste sites

Lack of patients? – a hypothesis for understanding discrepancies between hospital resources and productivity

BACKGROUND: Despite a substantial increase in hospital resources, increased hospital admissions and out-patient visits, long waiting lists have been a significant problem in Norwegian health care. A detailed analysis of the development in resource allocation and productivity at St. Olavs University Hospital in central Norway was therefore undertaken. METHODS: Resource allocation and patient volume was analysed during the period 1995 to 2001. Data were analysed both for emergency and elective admissions as well as outpatient visits specified into new referrals and follow-up consultations. RESULTS: Full time employee equivalents for doctors and nurses increased by 36.6% and 25.9%, respectively, and all employees by 28.1%. However, admitted patients, outpatient consultations and surgical procedures only increased by 10%, 15% and 8.3%, respectively. Thus, the productivity for each hospital employee, defined as operations pr. surgeon, outpatient consultations pr. doctor etc. was significantly reduced. A striking finding was that although the number of outpatient consultations increased, the number of new referrals actually went down and the whole increase in activity at the outpatient clinics could be explained by a substantial increase in follow-up consultations. This trend was more evident in the surgical departments, where some departments actually showed a reduction in total outpatient consultations. CONCLUSION: In view of the slow increase in hospital activity in spite of a significant increase in resources, it can be speculated that patient volume might be a limiting factor for hospital activity. The health market (patient population) might not be big enough in relation to the investments in increased production capacity (equipment and manpower)

Flood resilience community pathfinder evaluation: rapid evidence assessment

The increase in the risk of flooding as a result of extreme weather and climate change makes it essential for local authorities and communities to engage with this issue. Defra is providing grant funding to 13 local authorities throughout England under a new Flood Resilience Community Pathfinder (FRCP) scheme aimed at stimulating community action to increase resilience. The measures being developed include property-level protection, flood resilience groups, volunteer flood wardens and community champions, engagement with more vulnerable groups and efforts to increase financial resilience

Dietary soy and meat proteins induce distinct physiological and gene expression changes in rats

This study reports on a comprehensive comparison of the effects of soy and meat proteins given at the recommended level on physiological markers of metabolic syndrome and the hepatic transcriptome. Male rats were fed semi-synthetic diets for 1 wk that differed only regarding protein source, with casein serving as reference. Body weight gain and adipose tissue mass were significantly reduced by soy but not meat proteins. The insulin resistance index was improved by soy, and to a lesser extent by meat proteins. Liver triacylglycerol contents were reduced by both protein sources, which coincided with increased plasma triacylglycerol concentrations. Both soy and meat proteins changed plasma amino acid patterns. The expression of 1571 and 1369 genes were altered by soy and meat proteins respectively. Functional classification revealed that lipid, energy and amino acid metabolic pathways, as well as insulin signaling pathways were regulated differently by soy and meat proteins. Several transcriptional regulators, including NFE2L2, ATF4, Srebf1 and Rictor were identified as potential key upstream regulators. These results suggest that soy and meat proteins induce distinct physiological and gene expression responses in rats and provide novel evidence and suggestions for the health effects of different protein sources in human diets

Why it takes an 'ontological shock' to prompt increases in small firm resilience : sensemaking, emotions and flood risk

This article uses a sensemaking approach to understand small firms’ responses to the threat of external shocks. By analysing semi-structured interviews with owners of flooded small firms, we investigate how owners process flood experiences and explore why such experiences do not consistently lead to the resilient adaptation of premises. We, conclude that some of the explanation for low levels of adaptation relates to a desire to defend existing sensemaking structures and associated identities. Sensemaking structures are only revised if these structures are not critical to business identity, or if a flood constitutes an ‘ontological shock’ and renders untenable existing assumptions regarding long-term business continuity. This article has implications for adaptation to the growing risk of flooding, climate change and external shocks. Future research analysing external shocks would benefit from using a sensemaking approach and survey studies should include measurements of ‘ontological’ impact as well as material and financial damage. In addition, those designing information campaigns should take account of small firms’ resistance to information that threatens their existing sensemaking structures and social identities

The impact of the Barnett formula on the Scottish economy: endogenous population and variable formula proportions

The Barnett formula is the official basis upon which increments to public funds are allocated to the devolved regions of the UK for those parts of the budget that are administered locally. There is considerable controversy surrounding the implications of its strict application for the relevant regions. The existing literature focuses primarily on the equity of the spatial changes to government per capita expenditure that would accompany such a change. In contrast, in this paper we attempt to quantify the system-wide economic consequences-the real, relative resource squeeze that accompanies the financial relative squeeze-on one devolved region, Scotland. The analysis uses a multisectoral regional computable general equilibrium modelling approach. We highlight the importance of population endogeneity, particularly since the population proportions used in the formula are now regularly updated