Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory,comparative study

An inter-laboratory study of the accuracy of microbial source tracking (MST) methods was conducted using challenge fecal and sewage samples that were spiked into artificial freshwater and provided as unknowns (blind test samples) to the laboratories. The results of the Source Identification Protocol Project (SIPP) are presented in a series of papers that cover 41 MST methods. This contribution details the results of the virus and bacteriophage methods targeting human fecal or sewage contamination. Human viruses used as source identifiers included adenoviruses (HAdV), enteroviruses (EV), norovirus Groups I and II (NoVI and NoVII), and polyomaviruses (HPyVs). Bacteriophages were also employed, including somatic coliphages and F-specific RNA bacteriophages (FRNAPH) as general indicators of fecal contamination. Bacteriophage methods targeting human fecal sources included genotyping of FRNAPH isolates and plaque formation on bacterial hosts Enterococcus faecium MB-55, Bacteroides HB-73 and Bacteroides GB-124. The use of small sample volumes (≤50 ml) resulted in relatively insensitive theoretical limits of detection (10–50 gene copies or plaques × 50 ml⁻¹) which, coupled with low virus concentrations in samples, resulted in high false-negative rates, low sensitivity, and low negative predictive values. On the other hand, the specificity of the human virus methods was generally close to 100% and positive predictive values were ∼40–70% with the exception of NoVs, which were not detected. The bacteriophage methods were generally much less specific toward human sewage than virus methods, although FRNAPH II genotyping was relatively successful, with 18% sensitivity and 85% specificity. While the specificity of the human virus methods engenders great confidence in a positive result, better concentration methods and larger sample volumes must be utilized for greater accuracy of negative results, i.e. the prediction that a human contamination source is absent.     

Long-term effects of therapy on respiratory health

Only scant information is available on the long-term consequences to respiratory health of treatment with bronchodilators and oral corticosteroids. In the present study, we aimed to gain more information about these consequences. We examined 712 men working in the Paris area, by means of a subjective assessment of whether their respiratory health worsened or improved from 1960 to 1972, the decline in forced expiratory volume in one second (FEV1) over this time-period, and mortality from 1972 to 1992, in relation to respiratory therapy dispensed during a 2 year period in 1970-1971, as recorded in social security reimbursement records. As expected, subjects with respiratory symptoms or airflow limitation were more likely to have been prescribed respiratory therapy. After accounting for the effect of lung function level and smoking, subjects dispensed inhaled beta-agonists were likely to feel their condition had worsened and had a greater decline in FEV1 from 1960 to 1972. Among subjects with airflow limitation who reported asthma or persistent wheeze, having been dispensed oral corticosteroids on an intermittent basis was associated with improved survival (relative risk (RR) 0.32; 95% confidence interval (95% CI): 0.10-0.91) after adjusting for FEV1 level and smoking category. Our results add to the evidence that regular use of beta-agonist bronchodilators may be associated with adverse effects on respiratory health, whilst intermittent use of corticosteroids may be of long-term benefit.     

Land-use controls and the political process

The use of land-use control ordinances and regulatory agencies is seen by some as the answer to externality-related land-use problems. Such devices necessarily shift the allocation of land and related resources from the market to the realm of the politician. Because of this, regulatory bodies often are in position to confer large gains on selected individuals or groups and large costs on others. This has led to a variety of pressures on regulators by developers and others who would benefit from zoning changes and by other groups who oppose such change. In this paper, a detailed analysis of land-use control decisions in one city demonstrates that applicants for rezoning decisions who have significant economic and/or political power are able to obtain favorable rezoning decisions with a significantly higher frequency than do those who lack such power. One explanation for this phenomenon is that those with such power, which is often shared with the regulators, are able to use their influence and relationships with the members of the regulatory board in order to obtain decisions in their favor. Indeed, they may even use their power to insure that the requests of others are denied. Advocates of strong land-use controls should realize the potential resource allocation costs that tend to be associated with politically- rather than market-oriented decisions.     

A core breast biopsy diagnosis of invasive carcinoma allows for definitive surgical treatment planning

To evaluate whether the type of weight-bearing loading subjected to the skeleton during horseback-riding was associated with differences in bone mass and muscle strength of the thigh, we investigated bone mass and isokinetic muscle strength in 20 female horse riders (age 17.9 +/- 0.6 years) who were riding 7.0 +/- 3.4 hours/week, and 20 nonactive females (age 17.8 +/- 1.1 years). The groups were matched according to age, weight, and height. Areal bone mineral density was measured in total body, head, lumbar spine, right femoral neck, Ward's triangle, and trochanter, the whole dominant and nondominant humerus, and in specific sites in the right femur diaphysis, distal femur, proximal tibia, and tibia diaphysis using dual X-ray absorptiometry. Isokinetic concentric and eccentric peak torque of the quadricep and hamstring muscles were measured using an isokinetic dynamometer. There were no significant differences in bone mass between the horseback riders and nonactives at any site measured. The horse riders were significantly (P < 0.05-0.01) stronger in concentric hamstrings strength at 90 degrees/second and 225 degrees/second and in eccentric quadricep and hamstring strength at 90 degrees/second. Horseback riding in young females is associated with a high muscle strength of the thigh, but not with a high bone mass.     

Event memory: Temporal-order judgments of personal life experiences.

Three experiments with undergraduate subjects investigated the mental representations that people form when they recall and chronologically order their personal experiences. Subjects in each study first recalled five events that occurred to them in two general periods of their life (e.g., high school and college). Later, they saw pairs of these events and judged the order in which they occurred. It typically took less time to compare events that occurred in different time periods than events that occurred in the same period. However, response times depended on the serial positions of the compared events in each time period, and the distance between them, in ways that varied over the three experiments. These effects were interpreted in terms of a model of event memory and judgment proposed by Wyer, Shoben, Fuhrman, and Bodenhausen (1985). Specifically, subjects appear to organize the events they are asked to recall into categories defined by the periods of life in which they occurred and assign temporal codes to these categories. However, they do not perform a more detailed temporal coding of the events they recall unless a coherent temporal representation of these events is difficult to construct. A direct comparison between judgments of personal experiences and judgments of others' experiences suggested that people may make more detailed temporal coding of others' experiences than they do of their own. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

TreeMatrix: A Hybrid Visualization of Compound Graphs

We present a hybrid visualization technique for compound graphs (i.e. networks with a hierarchical clustering defined on the nodes) that combines the use of adjacency matrices, node‐link and arc diagrams to show the graph, and also combines the use of nested inclusion and icicle diagrams to show the hierarchical clustering. The graph visualized with our technique may have edges that are weighted and/or directed. We first explore the design space of visualizations of compound graphs and present a taxonomy of hybrid visualization techniques. We then present our prototype, which allows clusters (i.e. subtrees) of nodes to be grouped into matrices or split apart using a radial menu. We also demonstrate how our prototype can be used in the software engineering domain, and compare it to the commercial matrix‐based visualization tool Lattix using a qualitative user study.     

Effect of wheelchair headrest use on pediatric head and neck injury risk outcomes during rear impact

Comparative risks or benefits to wheelchair-seated pediatric occupants in motor vehicles associated with wheelchair headrest use during rear impact were evaluated using pediatric head and neck injury outcome measures. A Hybrid III 6-year-old anthropomorphic test device (ATD), seated in identical WC19-compliant pediatric manual wheelchairs, was used to measure head and neck response during a 25 km/h (16 mph), 11 g rear impact. ATD responses were evaluated across two test scenarios: three sled tests conducted without headrests, and three with slightly modified commercial headrests. Head and neck injury outcomes measures included: linear head acceleration, head injury criteria (HIC) values, neck injury criteria (N(ij)) values, and combined rotational head velocity and acceleration. Neck and head injury outcome measures improved by 34-70% in sled tests conducted with headrests compared to tests without headrests. Headrest use reduced N(ij) values and the likelihood of concussion from values above established injury thresholds to values below injury thresholds. Injury measure outcome reductions suggest lower head and neck injury risks for wheelchair-seated children using wheelchair-mounted headrests as compared to non-headrest users in rear impact. Use of relative comparisons across two test scenarios served to minimize effects of ATD biofidelity limitations.     

Optimizing the multipole‐to‐local operator in the fast multipole method for graphical processing units

This paper presents a number of algorithms to run the fast multipole method (FMM) on NVIDIA CUDA‐capable graphical processing units (GPUs) (Nvidia Corporation, Sta. Clara, CA, USA). The FMM is a class of methods to compute pairwise interactions between N particles for a given error tolerance and with computational cost of . The methods described in the paper are applicable to any FMMs in which the multipole‐to‐local (M2L) operator is a dense matrix and the matrix is precomputed. This is the case for example in the black‐box fast multipole method (bbFMM), which is a variant of the FMM that can handle large class of kernels. This example will be used in our benchmarks. In the FMM, two operators represent most of the computational cost, and an optimal implementation typically tries to balance those two operators. One is the nearby interaction calculation (direct sum calculation, line 29 in Listing 1), and the other is the M2L operation. We focus on the M2L. By combining multiple M2L operations and reordering the primitive loops of the M2L so that CUDA threads can reuse or share common data, these approaches reduce the movement of data in the GPU. Because memory bandwidth is the primary bottleneck of these methods, significant performance improvements are realized. Four M2L schemes are detailed and analyzed in the case of a uniform tree. The four schemes are tested and compared with an optimized, OpenMP parallelized, multi‐core CPU code. We consider high and low precision calculations by varying the number of Chebyshev nodes used in the bbFMM. The accuracy of the GPU codes is found to be satisfactory and achieved performance over 200 Gflop/s on one NVIDIA Tesla C1060 GPU (Nvidia Corporation, Sta. Clara, CA, USA). This was compared against two quad‐core Intel Xeon E5345 processors (Intel Corporation, Sta. Clara, CA, USA) running at 2.33 GHz, for a combined peak performance of 149 Gflop/s for single precision. For the low FMM accuracy case, the observed performance of the CPU code was 37 Gflop/s, whereas for the high FMM accuracy case, the performance was about 8.5 Gflop/s, most likely because of a higher frequency of cache misses. We also present benchmarks on an NVIDIA C2050 GPU (a Fermi processor)(Nvidia Corporation, Sta. Clara, CA, USA) in single and double precision. Copyright © 2011 John Wiley & Sons, Ltd.     

A comparison of phase imaging and quantitative susceptibility mapping in the imaging of multiple sclerosis lesions at ultrahigh field

Objective

The aim of this study was to compare the use of high-resolution phase and QSM images acquired at ultra-high field in the investigation of multiple sclerosis (MS) lesions with peripheral rings, and to discuss their usefulness for drawing inferences about underlying tissue composition.

Materials and methods

Thirty-nine Subjects were scanned at 7 T, using 3D T ₂*-weighted and T ₁-weighted sequences. Phase images were then unwrapped and filtered, and quantitative susceptibility maps were generated using a thresholded k-space division method. Lesions were compared visually and using a 1D profiling algorithm.

Results

Lesions displaying peripheral rings in the phase images were identified in 10 of the 39 subjects. Dipolar projections were apparent in the phase images outside of the extent of several of these lesions; however, QSM images showed peripheral rings without such projections. These projections appeared ring-like in a small number of phase images where no ring was observed in QSM. 1D profiles of six well-isolated example lesions showed that QSM contrast corresponds more closely to the magnitude images than phase contrast.

Conclusions

Phase images contain dipolar projections, which confounds their use in the investigation of tissue composition in MS lesions. Quantitative susceptibility maps correct these projections, providing insight into the composition of MS lesions showing peripheral rings.