A Modulated Closed Form solution for Quantitative Susceptibility Mapping - A thorough evaluation and comparison to iterative methods based on edge prior knowledge.

The aim of this study is to perform a thorough comparison of quantitative susceptibility mapping (QSM) techniques and their dependence on the assumptions made. The compared methodologies were: two iterative single orientation methodologies minimizing the l2, l1TV norm of the prior knowledge of the edges of the object, one over-determined multiple orientation method (COSMOS) and anewly proposed modulated closed-form solution (MCF). The performance of these methods was compared using a numerical phantom and in-vivo high resolution (0.65mm isotropic) brain data acquired at 7T using a new coil combination method. For all QSM methods, the relevant regularization and prior-knowledge parameters were systematically changed in order to evaluate the optimal reconstruction in the presence and absence of a ground truth. Additionally, the QSM contrast was compared to conventional gradient recalled echo (GRE) magnitude and R2* maps obtained from the same dataset. The QSM reconstruction results of the single orientation methods show comparable performance. The MCF method has the highest correlation (corrMCF=0.95, r(2)MCF =0.97) with the state of the art method (COSMOS) with additional advantage of extreme fast computation time. The l-curve method gave the visually most satisfactory balance between reduction of streaking artifacts and over-regularization with the latter being overemphasized when the using the COSMOS susceptibility maps as ground-truth. R2* and susceptibility maps, when calculated from the same datasets, although based on distinct features of the data, have a comparable ability to distinguish deep gray matter structures.

Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI.

Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the "HARDI reconstruction challenge" organized in the context of the "ISBI 2012" conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies.

Rapid bacterial genome sequencing: methods and applications in clinical microbiology.

The recent advances in sequencing technologies have given all microbiology laboratories access to whole genome sequencing. Providing that tools for the automated analysis of sequence data and databases for associated meta-data are developed, whole genome sequencing will become a routine tool for large clinical microbiology laboratories. Indeed, the continuing reduction in sequencing costs and the shortening of the 'time to result' makes it an attractive strategy in both research and diagnostics. Here, we review how high-throughput sequencing is revolutionizing clinical microbiology and the promise that it still holds. We discuss major applications, which include: (i) identification of target DNA sequences and antigens to rapidly develop diagnostic tools; (ii) precise strain identification for epidemiological typing and pathogen monitoring during outbreaks; and (iii) investigation of strain properties, such as the presence of antibiotic resistance or virulence factors. In addition, recent developments in comparative metagenomics and single-cell sequencing offer the prospect of a better understanding of complex microbial communities at the global and individual levels, providing a new perspective for understanding host-pathogen interactions. Being a high-resolution tool, high-throughput sequencing will increasingly influence diagnostics, epidemiology, risk management, and patient care.

The value of selected in vitro and in silico methods to predict acute oral toxicity in a regulatory context: results from the European Project ACuteTox.

ACuteTox is a project within the 6th European Framework Programme which had as one of its goals to develop, optimise and prevalidate a non-animal testing strategy for predicting human acute oral toxicity. In its last 6 months, a challenging exercise was conducted to assess the predictive capacity of the developed testing strategies and final identification of the most promising ones. Thirty-two chemicals were tested blind in the battery of in vitro and in silico methods selected during the first phase of the project. This paper describes the classification approaches studied: single step procedures and two step tiered testing strategies. In summary, four in vitro testing strategies were proposed as best performing in terms of predictive capacity with respect to the European acute oral toxicity classification. In addition, a heuristic testing strategy is suggested that combines the prediction results gained from the neutral red uptake assay performed in 3T3 cells, with information on neurotoxicity alerts identified by the primary rat brain aggregates test method. Octanol-water partition coefficients and in silico prediction of intestinal absorption and blood-brain barrier passage are also considered. This approach allows to reduce the number of chemicals wrongly predicted as not classified (LD50>2000 mg/kg b.w.).

Direct Determination of mechanical properties in shallow formations by (ultra) sonic methods

For several decades mechanical properties of shallow formations (soil) obtained by sonic to ultrasonic wave testing were reported to be greater than those based on mechanical tests. The present article relying on a statistical analysis of more than 300 tests shows that elastic moduli of the soil can indeed be obtained from (ultra)sonic tests and that they are identical to those resulting from mechanical tests.

Prognostic ability of practitioners of traditional arabic medicine: comparison with Western methods through a relative patient progress scale.

The ancient Greek medical theory based on balance or imbalance of humors disappeared in the western world, but does survive elsewhere. Is this survival related to a certain degree of health care efficiency? We explored this hypothesis through a study of classical Greco-Arab medicine in Mauritania. Modern general practitioners evaluated the safety and effectiveness of classical Arabic medicine in a Mauritanian traditional clinic, with a prognosis/follow-up method allowing the following comparisons: (i) actual patient progress (clinical outcome) compared with what the traditional 'tabib' had anticipated (= prognostic ability) and (ii) patient progress compared with what could be hoped for if the patient were treated by a modern physician in the same neighborhood. The practice appeared fairly safe and, on average, clinical outcome was similar to what could be expected with modern medicine. In some cases, patient progress was better than expected. The ability to correctly predict an individual's clinical outcome did not seem to be better along modern or Greco-Arab theories. Weekly joint meetings (modern and traditional practitioners) were spontaneously organized with a modern health centre in the neighborhood. Practitioners of a different medical system can predict patient progress. For the patient, avoiding false expectations with health care and ensuring appropriate referral may be the most important. Prognosis and outcome studies such as the one presented here may help to develop institutions where patients find support in making their choices, not only among several treatment options, but also among several medical systems.

Comparing Multilevel Clustering Methods on Weighted Graphs : The Case of Worldwide Air Passenger Traffic 2000-2004

Specific properties emerge from the structure of large networks, such as that of worldwide air traffic, including a highly hierarchical node structure and multi-level small world sub-groups that strongly influence future dynamics. We have developed clustering methods to understand the form of these structures, to identify structural properties, and to evaluate the effects of these properties. Graph clustering methods are often constructed from different components: a metric, a clustering index, and a modularity measure to assess the quality of a clustering method. To understand the impact of each of these components on the clustering method, we explore and compare different combinations. These different combinations are used to compare multilevel clustering methods to delineate the effects of geographical distance, hubs, network densities, and bridges on worldwide air passenger traffic. The ultimate goal of this methodological research is to demonstrate evidence of combined effects in the development of an air traffic network. In fact, the network can be divided into different levels of âeurooecohesionâeuro, which can be qualified and measured by comparative studies (Newman, 2002; Guimera et al., 2005; Sales-Pardo et al., 2007).

Imaging molasse and quaternary sediments in Lake Geneva, Switzerland, with 3-D high-resolution seismic reflection methods: A case study

A high-resolution three-dimensional (3-D) seismic reflection survey was conducted in Lake Geneva, near the city of Lausanne, Switzerland, as part of a project for developing such seismic techniques. Using a single 48-channel streamer, the 3-D site with an area of 1200 m x 600 m was surveyed in 10 days. A variety of complex geologic structures (e.g. thrusts, folds, channel-fill) up to similar to150 m below the water bottom were obtained with a 15 in.(3) water gun. The 3-D data allowed the construction of an accurate velocity model and the distinction of five major seismic facies within the Lower Freshwater Molasse (Aquitanian) and the Quaternary sedimentary units. Additionally, the Plateau Molasse (PM) and Subalpine Molasse (SM) erosional surface, "La Paudeze" thrust fault (PM-SM boundary) and the thickness of Quaternary sediments were accurately delineated in 3-D.

Test methods: anabolics.

In the International Olympic Committee (IOC) accredited laboratories, specific methods have been developed to detect anabolic steroids in athletes' urine. The technique of choice to achieve this is gas-chromatography coupled with mass spectrometry (GC-MS). In order to improve the efficiency of anti-doping programmes, the laboratories have defined new analytical strategies. The final sensitivity of the analytical procedure can be improved by choosing new technologies for use in detection, such as tandem mass spectrometry (MS-MS) or high resolution mass spectrometry (HRMS). A better sample preparation using immuno-affinity chromatography (IAC) is also a good tool for improving sensitivity. These techniques are suitable for the detection of synthetic anabolic steroids whose structure is not found naturally in the human body. The more and more evident use, on a large scale, of substances chemically similar to the endogenous steroids obliges both the laboratory and the sports authorities to use the steroid profile of the athlete in comparison with reference ranges from a population or with intraindividual reference values.