Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.

The European Prospective Investigation into Cancer and nutrition (EPIC) is a long-term, multi-centric prospective study in Europe investigating the relationships between cancer and nutrition. This study has served as a basis for a number of Genome-Wide Association Studies (GWAS) and other types of genetic analyses. Over a period of 5 years, 52,256 EPIC DNA samples have been extracted using an automated DNA extraction platform. Here we have evaluated the pre-analytical factors affecting DNA yield, including anthropometric, epidemiological and technical factors such as center of subject recruitment, age, gender, body-mass index, disease case or control status, tobacco consumption, number of aliquots of buffy coat used for DNA extraction, extraction machine or procedure, DNA quantification method, degree of haemolysis and variations in the timing of sample processing. We show that the largest significant variations in DNA yield were observed with degree of haemolysis and with center of subject recruitment. Age, gender, body-mass index, cancer case or control status and tobacco consumption also significantly impacted DNA yield. Feedback from laboratories which have analyzed DNA with different SNP genotyping technologies demonstrate that the vast majority of samples (approximately 88%) performed adequately in different types of assays. To our knowledge this study is the largest to date to evaluate the sources of pre-analytical variations in DNA extracted from peripheral leucocytes. The results provide a strong evidence-based rationale for standardized recommendations on blood collection and processing protocols for large-scale genetic studies.

Differential effects of high-fat diet on myocardial lipid metabolism in failing and nonfailing hearts with angiotensin II-mediated cardiac remodeling in mice.

Normal myocardium adapts to increase of nutritional fatty acid supply by upregulation of regulatory proteins of the fatty acid oxidation pathway. Because advanced heart failure is associated with reduction of regulatory proteins of fatty acid oxidation, we hypothesized that failing myocardium may not be able to adapt to increased fatty acid intake and therefore undergo lipid accumulation, potentially aggravating myocardial dysfunction. We determined the effect of high-fat diet in transgenic mice with overexpression of angiotensinogen in the myocardium (TG1306/R1). TG1306/R1 mice develop ANG II-mediated left ventricular hypertrophy, and at one year of age approximately half of the mice present heart failure associated with reduced expression of regulatory proteins of fatty acid oxidation and reduced palmitate oxidation during ex vivo working heart perfusion. Hypertrophied hearts from TG1306/R1 mice without heart failure adapted to high-fat feeding, similarly to hearts from wild-type mice, with upregulation of regulatory proteins of fatty acid oxidation and enhancement of palmitate oxidation. There was no myocardial lipid accumulation or contractile dysfunction. In contrast, hearts from TG1306/R1 mice presenting heart failure were unable to respond to high-fat feeding by upregulation of fatty acid oxidation proteins and enhancement of palmitate oxidation. This resulted in accumulation of triglycerides and ceramide in the myocardium, and aggravation of contractile dysfunction. In conclusion, hearts with ANG II-induced contractile failure have lost the ability to enhance fatty acid oxidation in response to increased fatty acid supply. The ensuing accumulation of lipid compounds may play a role in the observed aggravation of contractile dysfunction.

High prevalence of peripheral arterial disease in HIV-infected persons

BACKGROUND: Atherosclerosis has been assessed in human immunodeficiency virus (HIV)-infected persons by using various methods. Peripheral arterial disease (PAD) has not been evaluated, however. We studied the cross-sectional prevalence of lower limb PAD in an HIV-infected population. METHODS: PAD was assessed using the Edinburgh Claudication Questionnaire and by measuring the systolic ankle-brachial blood pressure index (ABI) at rest and after exercise. Patients with PAD were further evaluated by duplex scan of lower limb arteries. RESULTS: Ninety-two consecutive HIV-infected patients were evaluated (23.9% women; mean age, 49.5 years; 61.9% current smokers). Claudication was reported by 15.2% of the patients. PAD was found in 20.7% of the patients: 9.8% had an abnormal ABI (<0.90) at rest, and 10.9% had normal ABI at rest but a >25% decrease after exercise. Of the patients with PAD, 84.2% were investigated with duplex scan, all of whom had atherosclerotic occlusions or stenoses of the iliac or femoral arteries. Age, diabetes, smoking, and low CD4+ T lymphocyte counts were identified as independent predictors of PAD. CONCLUSIONS: The prevalence of symptomatic and asymptomatic PAD is high in the HIV-infected population and is much higher than expected (prevalence in the general population, approximately 3% at 60 years). This study suggests the presence of an epidemic of PAD approximately 20 years earlier in the HIV-infected than in the general population. Larger epidemiological studies are needed to better define risk factors and to evaluate whether PAD is associated with increased mortality, as it is in the general population.

Risk assessment of herbicide mixtures in a large European lake

Lake Geneva is one of the largest European lakes with a surface area of 580 km2. Its catchment area covers 7400 km2, of which approximately 20% is arable land. Monitoring campaigns have been carried out in 2004 and 2005 to determine the contamination of the lake by pesticides. The results highlight the widespread presence of herbicides in water, the measured concentrations for most substances remaining constant in 2004 and 2005. However, for some individual herbicides the concentrations increased drastically (e.g., the herbicide foramsulfuron). We assessed the environmental risk of the herbicides detected in the lake using water quality criteria recently determined for the Swiss environmental protection agency. Furthermore, we assessed the risk of herbicide mixtures, grouped based upon their mode of action. Generally, the risk estimated for all single substances is low, except for some sulfonylurea compounds. For these substances, the measured concentrations are higher than the predicted no-effect concentration. Impact on the flora of the lake can therefore not be excluded. When mixtures of pesticides with similar mode of action are taken into account, the risk remains lower than the mixture water quality criteria for all groups, but can reach as high as one third of this quality criteria. A further step would therefore be to assess the risk of the total pesticide mixture, including similar and dissimilar modes of action

Evaluation of a Bridge Constructed using High Performance Steel, May 2006

Of the approximately 25,000 bridges in Iowa, 28% are classified as structurally deficient, functionally obsolete, or both. Because many Iowa bridges require repair or replacement with a relatively limited funding base, there is a need to develop new bridge materials that may lead to longer life spans and reduced life-cycle costs. In addition, new and effective methods for determining the condition of structures are needed to identify when the useful life has expired or other maintenance is needed. Due to its unique alloy blend, high-performance steel (HPS) has been shown to have improved weldability, weathering capabilities, and fracture toughness than conventional structural steels. Since the development of HPS in the mid-1990s, numerous bridges using HPS girders have been constructed, and many have been economically built. The East 12th Street Bridge, which replaced a deteriorated box girder bridge, is Iowa’s first bridge constructed using HPS girders. The new structure is a two-span bridge that crosses I-235 in Des Moines, Iowa, providing one lane of traffic in each direction. A remote, continuous, fiber-optic based structural health monitoring (SHM) system for the bridge was developed using off-the-shelf technologies. In the system, sensors strategically located on the bridge collect raw strain data and then transfer the data via wireless communication to a gateway system at a nearby secure facility. The data are integrated and converted to text files before being uploaded automatically to a website that provides live strain data and a live video stream. A data storage/processing system at the Bridge Engineering Center in Ames, Iowa, permanently stores and processes the data files. Several processes are performed to check the overall system’s operation, eliminate temperature effects from the complete strain record, compute the global behavior of the bridge, and count strain cycles at the various sensor locations.

Factors associated with beliefs about adherence to non-pharmacological treatment of patients with heart failure

This study aimed at assessing beliefs about the benefits and barriers to adherence to daily self-monitoring of weight/edema in patients with heart failure, and the influence of demographic and clinical variables on those beliefs. 105 patients were interviewed. The mean of the subscales Benefits and Barriers were 20.2 (± 5.7) and 30.1 (±7.1), respectively. Patients perceived that adherence to daily self-monitoring of weight/edema could keep them healthy, improve their quality of life and decrease the chances of readmission. Approximately half of patients (46.7%) reported forgetting this measure. Those who controlled weight once a month were more likely to have barriers to adherence (OR= 6.6; IC 95% 1.9-13.8; p=0.01), showing this measure to be the main factor related to perceived barriers. Education in health can contribute with the development of strategies aimed at lowering barriers and increasing benefits of this control.

Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosome.

Cancer/testis (CT) genes are normally expressed in germ cells only, yet are reactivated and expressed in some tumors. Of the approximately 40 CT genes or gene families identified to date, 20 are on the X chromosome and are present as multigene families, many with highly conserved members. This indicates that novel CT gene families may be identified by detecting duplicated expressed genes on chromosome X. By searching for transcript clusters that map to multiple locations on the chromosome, followed by in silico analysis of their gene expression profiles, we identified five novel gene families with testis-specific expression and >98% sequence identity among family members. The expression of these genes in normal tissues and various tumor cell lines and specimens was evaluated by qualitative and quantitative RT-PCR, and a novel CT gene family with at least 13 copies was identified on Xq24, designated as CT47. mRNA expression of CT47 was found mainly in the testes, with weak expression in the placenta. Brain tissue was the only positive somatic tissue tested, with an estimated CT47 transcript level 0.09% of that found in testis. Among the tumor specimens tested, CT47 expression was found in approximately 15% of lung cancer and esophageal cancer specimens, but not in colorectal cancer or breast cancer. The putative CT47 protein consists of 288 amino acid residues, with a C-terminus rich in alanine and glutamic acid. The only species other than human in which a gene homologous to CT47 has been detected is the chimpanzee, with the predicted protein showing approximately 80% identity in its carboxy terminal region.

Insects associated with tropical foliage produced in the coffee growing region of Colombia

We conducted a survey of insects and pest management practices on 34 farms growing ornamental tropical foliage plants in the central coffee region of Colombia over two years. Tropical foliage provided habitat for a diverse range of insects. In total, phytophagous or detritivorous insects from six orders, 40 families and 62 genera were collected. The most common were Hemiptera (29 genera from 16 families), followed by Coleoptera (17 genera from 4 families), Diptera (5 genera from 5 families), Lepidoptera (5 genera from 4 families), Hymenoptera (3 genera from 2 families) and Orthoptera (2 genera from 2 families). The most common phytophagous species were leaf cutting ants (Atta and Acromyrmex spp.), leaf beetles (Chrysomelidae), leafhoppers (Cicadellidae), stinkbugs (Pentatomidae), squash bugs (Coreidae), tree hoppers (Membracidae) and plant hoppers (Fulgoridae). Beneficial insects identified from tropical foliage included predators and parasitoids amongst 5 orders, 12 families and 22 genera. The most abundant were predators among the Coccinellidae, Chrysopidae, Reduviidae, Lycidae and Formicidae but only low numbers of parasitoids (Ichneumonidae, Braconidae and Tachinidae) were collected. A pest management questionnaire given to growers revealed a preponderance of reliance on broad spectrum insecticides with a smaller number of growers (approximately one third) also using some biological control methods. Our survey contributes basic information regarding diversity of Neotropical insects associated with ornamental foliage plants.

Federal Highway Administration Finding of No Significant Impact Collins Road NE (Highway 100) Cedar Rapids, Linn County, Iowa, December 17, 2009

The proposed project consists of improving approximately 2.6 miles of Collins Road NE (Highway 100) in Cedar Rapids, Iowa. The project extends from the intersection of Center Point Road to approximately 750 feet east of its intersection with 1st Avenue.

Cloning and characterization of Helicobacter pylori succinyl CoA:acetoacetate CoA-transferase, a novel prokaryotic member of the CoA-transferase family.

Sequencing of a fragment of Helicobacter pylori genome led to the identification of two open reading frames showing striking homology with Coenzyme A (CoA) transferases, enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. The genes were present in all H. pylori strains tested by polymerase chain reaction or slot blotting but not in Campylobacter jejuni. Genes for the putative A and B subunits of H. pylori CoA-transferase were introduced into the bacterial expression vector pKK223-3 and expressed in Escherichia coli JM105 cells. Amino acid sequence comparisons, combined with measurements of enzyme activities using different CoA donors and acceptors, identified the H. pylori CoA-transferase as a succinyl CoA:acetoacetate CoA-transferase. This activity was consistently observed in different H. pylori strains. Antibodies raised against either recombinant A or B subunits recognized two distinct subunits of Mr approximately 26,000 and 24, 000 that are both necessary for H. pylori CoA-transferase function. The lack of alpha-ketoglutarate dehydrogenase and of succinyl CoA synthetase activities indicates that the generation of succinyl CoA is not mediated by the tricarboxylic acid cycle in H. pylori. We postulate the existence of an alternative pathway where the CoA-transferase is essential for energy metabolism.

Decreased Probability of Initial Pain Cessation in Classic Trigeminal Neuralgia Treated With Gamma Knife Surgery in Case of Previous Microvascular Decompression: A Prospective Series of 45 Patients With >1 Year of Follow-up.

BACKGROUND: Microvascular decompression (MVD) is the reference technique for pharmacoresistant trigeminal neuralgia (TN). OBJECTIVE: To establish whether the safety and efficacy of Gamma Knife surgery for recurrent TN are influenced by prior MVD. METHODS: Between July 1992 and November 2010, 54 of 737 patients (45 of 497 with >1 year of follow-up) had a history of MVD (approximately half also with previous ablative procedure) and were operated on with Gamma Knife surgery for TN in the Timone University Hospital. A single 4-mm isocenter was positioned in the cisternal portion of the trigeminal nerve at a median distance of 7.6 mm (range, 3.9-11.9 mm) anterior to the emergence of the nerve. A median maximum dose of 85 Gy (range, 70-90 Gy) was delivered. RESULTS: The median follow-up time was 39.5 months (range, 14.1-144.6 months). Thirty-five patients (77.8%) were initially pain free in a median time of 14 days (range, 0-180 days), much lower compared with our global population of classic TN (P = .01). Their actuarial probabilities of remaining pain-free without medication at 3, 5, 7, and 10 years were 66.5%, 59.1%, 59.1%, and 44.3%. The hypoesthesia actuarial rate at 1 year was 9.1% and remained stable until 12 years (median, 8 months). CONCLUSION: Patients with previous MVD showed a significantly lower probability of initial pain cessation compared with our global population with classic TN (P = .01). The toxicity was low (only 9.1% hypoesthesia); furthermore, no patient reported bothersome hypoesthesia. However, the probability of maintaining pain relief without medication was 44.3% at 10 years, similar to our global series of classic TN (P = .85). ABBREVIATIONS: BNI, Barrow Neurological InstituteCI, confidence intervalCTN, classic trigeminal neuralgiaGKS, Gamma Knife surgeryHR, hazard ratioMVD, microvascular decompressionTN, trigeminal neuralgia.

Risk Assessement of Herbicide Mixtures

Lake Geneva is one of the largest European lakes with a surface area of 580 km2. Its catchment area covers 7400 km2, of which approximately 20% is arable land. Monitoring campaigns have been carried out in 2004 and 2005 to determine the contamination of the lake by pesticides. The results highlight the widespread presence of herbicides in water, the measured concentrations for most substances remaining constant in 2004 and 2005. However, for some individual herbicides the concentrations increased drastically (e.g., the herbicide foramsulfuron). We assessed the environmental risk of the herbicides detected in the lake using water quality criteria recently determined for the Swiss environmental protection agency. Furthermore, we assessed the risk of herbicide mixtures, grouped based upon their mode of action. Generally, the risk estimated for all single substances is low, except for some sulfonylurea compounds. For these substances, the measured concentrations are higher than the predicted no-effect concentration. Impact on the flora of the lake can therefore not be excluded. When mixtures of pesticides with similar mode of action are taken into account, the risk remains lower than the mixture water quality criteria for all groups, but can reach as high as one third of this quality criteria. A further step would therefore be to assess the risk of the total pesticide mixture, including similar and dissimilar modes of action.

Road Safety Audit Report for US 61 from the ECL of Muscatine to the WCL of, 2008

U.S. Highway 61 between Muscatine and Davenport, Iowa, is a four-lane divided section of road approximately 21 miles in length. This section was found to be among the top 5% of Iowa roadways for single-vehicle run-off-road, impaired driver, unbelted driver, and speed-related crashes for the period of 2001 through 2005. A road safety audit of this corridor was deemed appropriate by the Iowa Department of Transportation’s Office of Traffic and Safety. Staff and officials from the Iowa Department of Transportation (Iowa DOT), Iowa State Patrol, Governor’s Traffic Safety Bureau, Federal Highway Administration, Center for Transportation Research and Education, and several local law enforcement and transportation agencies met to review crash data and discuss potential safety improvements to US 61. This report outlines the findings and recommendations of the road safety audit team to address the safety concerns on this US 61 corridor and explains several selected mitigation strategies.

Remote Continuous Evaluation of a Bridge Constructed Using High-Performance Steel, 2006

Of the approximately 25,000 bridges in Iowa, 28% are classified as structurally deficient, functionally obsolete, or both. The state of Iowa thus follows the national trend of an aging infrastructure in dire need of repair or replacement with a relatively limited funding base. Therefore, there is a need to develop new materials with properties that may lead to longer life spans and reduced life-cycle costs. In addition, new methods for determining the condition of structures are needed to monitor the structures effectively and identify when the useful life of the structure has expired or other maintenance is needed. High-performance steel (HPS) has emerged as a material with enhanced weldability, weathering capabilities, and fracture toughness compared to conventional structural steels. In 2004, the Iowa Department of Transportation opened Iowa's first HPS girder bridge, the East 12th Street Bridge over I-235 in Des Moines, Iowa. The objective of this project was to evaluate HPS as a viable option for use in Iowa bridges with a continuous structural health monitoring (SHM) system. The scope of the project included documenting the construction of the East 12th Street Bridge and concurrently developing a remote, continuous SHM system using fiber-optic sensing technology to evaluate the structural performance of the bridge. The SHM system included bridge evaluation parameters, similar to design parameters used by bridge engineers, for evaluating the structure. Through the successful completion of this project, a baseline of bridge performance was established that can be used for continued long-term monitoring of the structure. In general, the structural performance of the HPS bridge exceeded the design parameters and is performing well. Although some problems were encountered with the SHM system, the system functions well and recommendations for improving the system have been made.

U.S. 61 From Memorial Park Road in Burlington North to 1 Mile North of IA 78 in Louisa County. Des Moines & Louisa County, Iowa NHS-061-2(50) - 19-58, 2015

Iowa Department of Transportation (Iowa DOT) has re-initiated planning and preliminary design studies to improve U.S. 61 from Memorial Park Road in Burlington north to 1-mile north of IA 78 in Louisa County. The proposed project consists of improving approximately 18 miles of roadway from 2-lanes to 4-lanes and evaluating a potential bypass around Mediapolis.