FAM-MDR: a flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals

We propose a novel multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees, FAM-MDR. It combines features of the Genome-wide Rapid Association using Mixed Model And Regression approach (GRAMMAR) with Model-Based MDR (MB-MDR). We focus on continuous traits, although the method is general and can be used for outcomes of any type, including binary and censored traits. When comparing FAM-MDR with Pedigree-based Generalized MDR (PGMDR), which is a generalization of Multifactor Dimensionality Reduction (MDR) to continuous traits and related individuals, FAM-MDR was found to outperform PGMDR in terms of power, in most of the considered simulated scenarios. Additional simulations revealed that PGMDR does not appropriately deal with multiple testing and consequently gives rise to overly optimistic results. FAM-MDR adequately deals with multiple testing in epistasis screens and is in contrast rather conservative, by construction. Furthermore, simulations show that correcting for lower order (main) effects is of utmost importance when claiming epistasis. As Type 2 Diabetes Mellitus (T2DM) is a complex phenotype likely influenced by gene-gene interactions, we applied FAM-MDR to examine data on glucose area-under-the-curve (GAUC), an endophenotype of T2DM for which multiple independent genetic associations have been observed, in the Amish Family Diabetes Study (AFDS). This application reveals that FAM-MDR makes more efficient use of the available data than PGMDR and can deal with multi-generational pedigrees more easily. In conclusion, we have validated FAM-MDR and compared it to PGMDR, the current state-of-the-art MDR method for family data, using both simulations and a practical dataset. FAM-MDR is found to outperform PGMDR in that it handles the multiple testing issue more correctly, has increased power, and efficiently uses all available information.

Le fixateur externe dans les lésions traumatiques graves du bassin: résultats à propos de 20 cas consécutifs [External fixator in severe traumatic injuries of the pelvis: results apropos of 20 consecutive cases]

From August 91 to December 94, 20 external fixators were used for severely injured patients (avg. ISS 25.2). The fractures were essentially open book with or without lateral compression and vertical lesions. The indication for fixation was treatment of shock and stabilization in 8 cases, stabilization alone in 9 cases, and in 3 cases as complementary fixation after internal fixation of posterior lesions. The fixation of the pelvis was effective on the amount of blood loss. One acetabulum fracture required surgery, two patients had internal fixation for loss of reduction and two others for late pubic and posterior pain. The clinical results are good; they are more related to the severity of the initial lesion than to the mode of fixation or the quality of the reduction. No superficial sepsis or osteitis was observed in relation to the pins.

Decreased glucose-induced thermogenesis after weight loss in obese subjects: a predisposing factor for relapse of obesity?

Glucose-induced thermogenesis (GIT) after a 100-g oral glucose load was measured by continuous indirect calorimetry in 32 nondiabetic and diabetic obese subjects and compared to 17 young and 13 middle aged control subjects. The obese subjects were divided into three groups: A (n = 12) normal glucose tolerance, B (n = 13) impaired glucose tolerance, and C (n = 7) diabetics, and were studied before and after a body weight loss ranging from 9.6 to 33.5 kg consecutive to a 4 to 6 months hypocaloric diet. GIT, measured over 3 h and expressed as percentage of the energy content of the load, was significantly reduced in obese groups A and C (6.2 +/- 0.6, and 3.8 +/- 0.7%, respectively) when compared to their age-matched control groups: 8.6 +/- 0.7 (young) and 5.8 +/- 0.3% (middle aged). Obese group B had a GIT of 6.1 +/- 0.6% which was lower than that of the young control group but not different from the middle-aged control group. After weight loss, GIT in the obese was further reduced in groups A and B than before weight loss: ie, 3.4 +/- 0.6 (p less than 0.001), 3.7 +/- 0.5 (p less than 0.01) respectively, whereas in group C, weight loss induced no further diminution in GIT (3.8 +/- 0.6%). These results support the concept of a thermogenic defect after glucose ingestion in obese individuals which is not the consequence of their excess body weight but may be one of the factors favoring the relapse of obesity after weight loss.

Beta-lactam resistance mechanisms of methicillin-resistant Staphylococcus aureus.

In vitro and in vivo activity of amoxicillin and penicillin G alone or combined with a penicillinase inhibitor (clavulanate) were tested against five isogenic pairs of methicillin-resistant Staphylococcus aureus (MRSA) producing or not producing penicillinase. Loss of the penicillinase plasmid caused an eight times or greater reduction in the MICs of amoxicillin and penicillin G (from greater than or equal to 64 to 8 micrograms/ml), but not of the penicillinase-resistant drugs methicillin and cloxacillin (greater than or equal to 64 micrograms/ml). This difference in antibacterial effectiveness correlated with a more than 10 times greater penicillin-binding protein 2a affinity of amoxicillin and penicillin G than of methicillin and a greater than or equal to 90% successful amoxicillin treatment of experimental endocarditis due to penicillinase-negative MRSA compared with cloxacillin, which was totally ineffective (P less than .001). Amoxicillin was also effective against penicillinase-producing parent MRSA, provided it was combined with clavulanate. Penicillinase-sensitive beta-lactam antibiotics plus penicillinase inhibitors might offer a rational alternative treatment for MRSA infections.

Reduction of ARNT in myeloid cells causes immune suppression and delayed wound healing.

Aryl hydrocarbon receptor nuclear translocator (ARNT) is a transcription factor that binds to partners to mediate responses to environmental signals. To investigate its role in the innate immune system, floxed ARNT mice were bred with lysozyme M-Cre recombinase animals to generate lysozyme M-ARNT (LAR) mice with reduced ARNT expression. Myeloid cells of LAR mice had altered mRNA expression and delayed wound healing. Interestingly, when the animals were rendered diabetic, the difference in wound healing between the LAR mice and their littermate controls was no longer present, suggesting that decreased myeloid cell ARNT function may be an important factor in impaired wound healing in diabetes. Deferoxamine (DFO) improves wound healing by increasing hypoxia-inducible factors, which require ARNT for function. DFO was not effective in wounds of LAR mice, again suggesting that myeloid cells are important for normal wound healing and for the full benefit of DFO. These findings suggest that myeloid ARNT is important for immune function and wound healing. Increasing ARNT and, more specifically, myeloid ARNT may be a therapeutic strategy to improve wound healing.

Extreme population differentiation in vulnerable slavemaking ant with fragmented distribution

Understanding levels of population differentiation and inbreeding are important issues in conservation biology, especially for social Hymenoptera with fragmented and small population sizes. Isolated populations are more vulnerable to genetic loss and extinction than those with extended continuous distributions. However, small populations are not always a consequence of a recent reduction of their habitat. Thus, determining the history of population isolation and current patterns of genetic variation of a species is crucial for its conservation. Rossomyrmex minuchae is a slave-making ant with patchy distribution in South Eastern Spain and is classified as vulnerable by the IUCN. In contrast, the other three known species of the genus are presumed to show more uniform distributions. Here we investigate the genetic diversity and population structure of R. minuchae and compare it with that found in two other species of the genus: R. anatolicus and R. quandratinodum. We conclude that although genetic diversity of R. minuchae is low, there is no evidence of a recent bottleneck, suggesting a gradual and natural fragmentation process. We also show extreme population differentiation at nuclear and mitochondrial markers, and isolation by distance at a local scale. Despite some evidence for inbreeding and low genetic variation within populations, we found almost no diploid males, a finding which contrasts with that expected in inbred Hymenoptera with single locus complementary sex determination. This could mean that sex is determined by another mechanism. We argue that continued low population size means that detrimental effects of inbreeding and low genetic variation are likely in the future. We suggest that a policy of artificial gene flow aimed at increasing within population variation is considered as a management option.

NR2A at CA1 synapses is obligatory for the susceptibility of hippocampal plasticity to sleep loss.

A loss in the necessary amount of sleep alters expression of genes and proteins implicated in brain plasticity, but key proteins that render neuronal circuits sensitive to sleep disturbance are unknown. We show that mild (4-6 h) sleep deprivation (SD) selectively augmented the number of NR2A subunits of NMDA receptors on postsynaptic densities of adult mouse CA1 synapses. The greater synaptic NR2A content facilitated induction of CA3-CA1 long-term depression in the theta frequency stimulation range and augmented the synaptic modification threshold. NR2A-knock-out mice maintained behavioral response to SD, including compensatory increase in post-deprivation resting time, but hippocampal synaptic plasticity was insensitive to sleep loss. After SD, the balance between synaptically activated and slowly recruited NMDA receptor pools during temporal summation was disrupted. Together, these results indicate that NR2A is obligatory for the consequences of sleep loss on hippocampal synaptic plasticity. These findings could advance pharmacological strategies aiming to sustain hippocampal function during sleep restriction.

Asphalt Stabilization (Asphadur)/Reduction of Reflection Cracks (Monsanto Bidim Synthetic Fabric), HR-511, 1979

ASPHALT STABILIZATION (ASPHADUR): Asphadur (now called 3M Additive 5990) was incorporated into asphaltic concrete on a lane delineation, AC resurfacing, project in Council Bluffs. The experimental feature was included in the eastbound lanes of Interstate 480, beginning at the bridge over the Missouri River and ending at the bridge over North 41st Street. The project was constructed in October 1979. The objective of the project was to investigate the manufacturer's claims of improved strength, stability and durability of an asphalt mix. REDUCTION OF REFLECTION CRACKS (MONSANTO BIDIM SYNTHETIC FABRIC): A lane delineation project was constructed in the eastbound lanes of Interstate 480 in Council Bluffs. A synthetic fabric, Monsanto Bidim C-28, was placed between the portland cement concrete and two inches of Type A asphaltic concrete resurfacing containing Asphadur. The experimental feature began at the bridge over the Missouri River and ended at the bridge over North 41st Street. The project was constructed in October 1979. The objective of this experimental project was to determine the effectiveness of the fabric in reducing reflective cracking in an asphaltic concrete overlay.

Reduction of Concrete Deterioration by Ettringite Using Crystal Growth Inhibition Techniques: Part II Field Evaluation of Inhibitor Effectiveness, TR-469, 2004

The effects of diethylenetriaminpenta(methylenephosphonic acid) (DTPMP), a phosphonate inhibitor, on the growth of delayed ettringite have been evaluated using concrete in highway US 20 near Williams, Iowa, and the cores of six highways subject to moderate (built in 1992) or minor (built in 1997) deterioration. Application of 0.01 and 0.1 vol. % DTPMP to cores was made on a weekly or monthly basis for one year under controlled laboratory-based freeze-thaw and wet-dry conditions over a temperature range of -15 degrees to 58 degrees C to mimic extremes in Iowa roadway conditions. The same concentrations of phosphonate were also applied to cores left outside (roof of Science I at Iowa State University) over the same period of time. Nineteen applications of 0.1 vol. % DTPMP with added deicing salt solution (about 23 weight % NACL) were made to US 20 during the winters of 2003 and 2004. In untreated samples, air voids, pores, and occasional cracks are lined with acicular ettringite crystals (up to 50 micrometers in length) whereas air voids, pores, and cracks in concrete from the westbound lane of US 20 are devoid of ettringite up to a depth of about 0.5 mm from the surface of the concrete. Ettringite is also absent in zones up to 6 mm from the surface of concrete slabs placed on the roof of Science I and cores subject to laboratory-based freeze-thaw experiments. In these zones, the relatively high concentration of DTPMP caused it to behave as a chelator. Stunted ettringite crystals 5 to 25 micrometers in length, occasionally coated with porlandite, form on the margins of these zones indicating that in these areas DTPMP behaved as an inhibitor due to a reduction in the concentration of phosphonate. Analyses of mixes of ettringite and DTPMP using electrospray mass spectrometry suggests that the stunting of ettringite growth is caused by the adsorption of a Ca2+ ion and a water molecule to deprotonated DTPMP on the surface of the {0001} face of ettringite. It is anticipated that by using a DTPMP concentration of between 0.001 and 0.01 vol. % for the extended life of a highway (i.e. >20 years), deterioration caused by the expansive growth of ettringite will be markedly reduced.

Investigation of Materials for the Reduction and Prevention of Corrosion on Highway Maintenance Equipment, TR-472, 2009

The issue of corrosion of winter maintenance equipment is becoming of greater concern because of the increased use of liquid solutions of ice control chemicals, as opposed to their application in solid form. Being in liquid form, the ice control chemicals can more easily penetrate into the nooks and crannies on equipment and avoid being cleansed from the vehicle. Given this enhanced corrosive ability, methods must be found to minimize corrosion. The methods may include coatings, additives, cleansing techniques, other methods, and may also include doing nothing, and accepting a reduced equipment lifetime as a valid (perhaps) trade off with the enhanced benefits of using liquid ice control chemicals. In reality, some combination of these methods may prove to be optimal. Whatever solutions are selected, they must be relatively cheap and durable. The latter point is critical because of the environment in which maintenance trucks operate, in which scrapes, scratches and dents are facts of life. Protection methods that are not robust simply will not work. The purpose of this study is to determine how corrosion occurs on maintenance trucks, to find methods that would minimize the major corrosion mechanisms, and to

The ADVANCE trial: clarifying the role of perindopril/indapamide fixed-dose combination in the reduction of cardiovascular and renal events in patients with diabetes mellitus.

Patients with type 2 diabetes mellitus exhibit a marked increase in cardiovascular and renal risk. A number of interventional trials have shown that these patients benefit greatly from aggressive BP lowering, especially when the drug regimen comprises an inhibitor of the renin-angiotensin system. The results of the placebo-controlled ADVANCE (Action in Diabetes and Vascular disease: PreterAx and DiamicroN MR Controlled Evaluation) trial, conducted in patients with type 2 diabetes, are exemplary in this respect. The systematic use of a fixed-dose combination containing the ACE inhibitor perindopril and the diuretic indapamide afforded substantial protection against cardiovascular mortality and myocardial infarction, while providing important renoprotection, reducing the development of micro- and macroalbuminuria, and allowing regression of nephropathy. The beneficial effects were obtained regardless of baseline BP and whether or not the patients were receiving antihypertensive therapy.

Examination of Curing Criteria for Cold In-Place Recycling (Phase 3: Calibration of Moisture Loss Indices and Development of Stiffness Gain Model), TR-609, 2011

In the previous study, moisture loss indices were developed based on the field measurements from one CIR-foam and one CIR-emulsion construction sites. To calibrate these moisture loss indices, additional CIR construction sites were monitored using embedded moisture and temperature sensors. In addition, to determine the optimum timing of an HMA overlay on the CIR layer, the potential of using the stiffness of CIR layer measured by geo-gauge instead of the moisture measurement by a nuclear gauge was explored. Based on the monitoring the moisture and stiffness from seven CIR project sites, the following conclusions are derived: 1. In some cases, the in-situ stiffness remained constant and, in other cases, despite some rainfalls, stiffness of the CIR layers steadily increased during the curing time. 2. The stiffness measured by geo-gauge was affected by a significant amount of rainfall. 3. The moisture indices developed for CIR sites can be used for predicting moisture level in a typical CIR project. The initial moisture content and temperature were the most significant factors in predicting the future moisture content in the CIR layer. 4. The stiffness of a CIR layer is an extremely useful tool for contractors to use for timing their HMA overlay. To determine the optimal timing of an HMA overlay, it is recommended that the moisture loss index should be used in conjunction with the stiffness of the CIR layer.

Laboratory Investigation of Concrete Beam-End Treatments, RB08-013, 2015

The ends of prestressed concrete beams under expansion joints are often exposed to moisture and chlorides. Left unprotected, the moisture and chlorides come in contact with the ends of the prestressing strands and/or the mild reinforcing, resulting in corrosion. Once deterioration begins, it progresses unless some process is employed to address it. Deterioration can lead to loss of bearing area and therefore a reduction in bridge capacity. Previous research has looked into the use of concrete coatings (silanes, epoxies, fiber-reinforced polymers, etc.) for protecting prestressed concrete beam ends but found that little to no laboratory research has been done related to the performance of these coatings in this specific type of application. The Iowa Department of Transportation (DOT) currently specifies coating the ends of exposed prestressed concrete beams with Sikagard 62 (a high-build, protective, solvent-free, epoxy coating) at the precast plant prior to installation on the bridge. However, no physical testing of Sikagard 62 in this application has been completed. In addition, the Iowa DOT continues to see deterioration in the prestressed concrete beam ends, even those treated with Sikagard 62. The goals of this project were to evaluate the performance of the Iowa DOT-specified beam-end coating as well as other concrete coating alternatives based on the American Association of State Highway and Transportation Officials (AASHTO) T259-80 chloride ion penetration test and to test their performance on in-service bridges throughout the duration of the project. In addition, alternative beam-end forming details were developed and evaluated for their potential to mitigate and/or eliminate the deterioration caused by corrosion of the prestressing strands on prestressed concrete beam ends used in bridges with expansion joints. The alternative beam-end details consisted of individual strand blockouts, an individual blockout for a cluster of strands, dual blockouts for two clusters of strands, and drilling out the strands after they are flush cut. The goal of all of the forming alternatives was to offset the ends of the prestressing strands from the end face of the beam and then cover them with a grout/concrete layer, thereby limiting or eliminating their exposure to moisture and chlorides.